TICOR book

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TICOR book

Table of ContentsOVERVIEW OF TOOLSRole in projectBrief descriptionDATA ANALYSIS TOOLSRelational databaseGeographic information systemAPPLICATION TO SYSTEM DELIMITATION AND MORPHOLOGYTransitional water upstream limitsTransitional water downstream limitsCoastal water limitsMorphological parametersTYPOLOGY TOOLSECOLOGICAL STATUS EVALUATION TOOLSPelagic classification toolsBenthic classification toolsKEY REFERENCES11111212121314141515151616161718SYSTEMS, LIMITS AND MORPHOLOGYINTRODUCTION AND OBJECTIVESMETHODS AND CRITERIAReview of available approachesTheoretical basisAdvantages of the proposed definitionData requirementsMETHODSUpstream limitsPractical questionsAlternative approachesDownstream limitsSYSTEM SELECTION METHODOLOGYRESULTS1919191920212121212222232324


Table of ContentsPRESSURES AND IMPACTSPolluting emissionsWater regimeMorphologyBiologyReportingKEY REFERENCES87878989909091GENERAL CONCLUSIONS93


Executive SummaryPortugal has a number of important estuaries,which fall under the category of transitionalwaters – two of these, and parts of the riverswhich flow into them, form the northwestern andsoutheastern borders with Spain. Portugal has anextensive coastal area, which delimits the countryto the west and to the south.The Typology and Reference Conditions (TICOR)study aimed to provide a framework for appropriatecoastal management in Portugal, following therequirements of the Water Framework Directive.The team carrying out this work reviewed a broadrange of issues, ranging from classification ofdifferent systems, division into system types, andexamination of approaches to ecological qualitystatus and the definition of reference conditions fortransitional and coastal waters.In order to address some of these issues, theTICOR project was carried out.The key outputs of TICOR are presented in thisbook, which begins with a brief introduction toTICOR objectives• Develop an integrated approach for all Portuguese coastal and transitional waters for the application ofthe Water Framework Directive (WFD)• Provide the data framework and methodology for delimiting and typing Portuguese coastal andtransitional systems• Assemble the data required for WFD typology and first generation (G1) reference conditions, based on WFDcriteria and on the guidance provided by the Common Implementation Strategy working group COAST• Deliver a set of maps for typology of a key subset of Portuguese coastal and transitional waters• Derive a set of G1 reference conditions for Portuguese coastal and transitional types• Review the special issues of Heavily Modified Water Bodies and of Pressures and their application toPortuguese coastal and transitional watersthe WFD, and to the main aspects concerningtransitional and coastal waters, and follows with afurther seven chapters. Every effort has been madeto allow each chapter to be readable on its own,i


Executive Summaryby including the basic components of the theme,from concepts to methods and results. The toolschapter provides an overview of the techniquesused for the different parts of the work.IntroductionWFD and guidance & key objectivesMethodologyDetails on the TICOR processToolsSummary of tools used in TICORSystems, limits & morphologyDefinitions for transitional & coastal waters, GISpresentation of areas and volumesTypologyClassification of transitional & coastal waters intoseven typesPelagic reference conditionsReview of the state of the art for classificationtools, and suggested approaches for defining firstgeneration pelagic reference conditionsBenthic reference conditionsReview of the state of the art for classificationtools, and suggested approaches for defining firstgeneration benthic reference conditionsSpecial issuesHeavily Modified Water Bodies and generalapproach to environmental pressuresA summary of the key outputs and findings ofTICOR are presented below.DataOver 600,000 records of data for Portuguesetransitional and coastal waters have beenarchived in relational databases during theproject. These are available on the internet, andcontain parameters ranging from water andsediment quality to species lists, covering tenii


Executive SummaryFigure 1. Areas and volumes of TICOR systems.System name Classification Area (km 2 ) Volume (10 6 m 3 )Minho estuary Transitional 23 67Lima estuary Transitional 5 19Douro estuary Transitional 5 39Ria de Aveiro Transitional 60 84Mondego estuary Transitional 9 21Tagus estuary Transitional 330 2 200Sado estuary Transitional 170 850Mira estuary Transitional 3 17Guadiana estuary Transitional 18 96Ria Formosa Coastal 49 92Exposed Atlantic coast Coastal 3 200 195 000Moderately exposed Atlantic coast Coastal 4 200 295 900Sheltered Atlantic coast Coastal 1 000 27 600Note: Different colours correspond to different types.transitional and coastal waters, and in somecases spanning over seventy years. These datawere the foundation for the work which has beendeveloped, and are an important referencecollection of historical information on which futuremonitoring and research activities may build.Systems, limits and morphologyTICOR addressed ten transitional and inshorecoastal systems, as well as the coastline ofcontinental Portugal (Figure 1). The project didnot consider the areas of Madeira and Azores.A geographic information system (GIS) wasdeveloped for all the systems, and was used as aframework for the subsequent definition of limits,areas and volumes.From a total of 44 transitional or coastal systemsin Portugal, about half are in class A (≤ 0.3 km 2 ).The other 48% are distributed in other classes.Class D (≥ 1.0 km 2 ) is the most representative ofthese.The systems studied in TICOR, together with theirclassification into transitional or coastal watersand morphological data, are shown in Figure 1.iii


Executive SummaryTypologySeven different types of transitional and coastalwaters were defined for Portugal, based on theconsideration that the number of types should berelatively small but should accurately reflect theexisting diversity of systems (Figure 2).Two transitional water types were defined,corresponding to estuarine systems from thenorthern and southern parts of Portugal. Type A2,mesotidal well-mixed estuary with irregular riverdischarge, is envisaged to be almost unique inthe European Union, due to the combination ofhighly variable freshwater discharge and mesotidalregime. Additionally, two semi-enclosed coastaltypes were defined, as well as three open coastaltypes, which were judged to be sufficient todescribe the entire Atlantic coastline. Of thesethree, type A6, mesotidal moderately exposedAtlantic coast, is considered to be unique to theEuropean Union, because it combines coldernorth-east Atlantic and warmer Mediterraneaninfluences with the dynamics of a narrow shelf.The type names and descriptions are shown inFigure 2.The rationale for each type is explained in theTypology chapter, and the areas and volumes forthe different types were determined with basis onthe GIS. Some results are presented also on thedistribution of these morphological data amongtypes, and a discussion of types which maypotentially be common to other EU member statesis made. The most likely candidate types are: A1,A3, A5 and A7.Figure 2. Proposed typology and classification of systems larger that 1 km 2 .Type Descriptor Systems larger than 1 km 2A1 Mesotidal stratified estuary Minho estuaryLima estuaryDouro estuaryLeça estuaryA2 Mesotidal well-mixed estuary Ria de Aveirowith irregular river dischargeMondego estuaryTagus estuarySado estuaryMira estuaryArade estuaryGuadiana estuaryA3 Mesotidal semi-enclosed lagoon Óbidos lagoonAlbufeira lagoonSt. André lagoonA4 Mesotidal shallow lagoon Ria de AlvorRia FormosaA5 Mesotidal exposed Atlantic coast From the Minho estuary until Cabo CarvoeiroA6 Mesotidal moderately exposed From Cabo Carvoeiro until Ponta da PiedadeAtlantic coastA7 Mesotidal sheltered coast From Ponta da Piedade until Vila Real de Sto. AntónioNote: TICOR systems shown in blue.iv


Executive SummaryMain findings for pelagic reference coditions• There are sufficient data in most cases for establishing reference conditions for phytoplantonabundance, biomass and composition. Some gaps exist for type A1 and for open coastal waters• The supporting quality element nutrients should be measured in order to monitor elemental ratios, andto support the evaluation of pressures, but no clear link between dissolved nutrients in the watercolumn and phytoplankton biomass and abundance could be established• Phytoplankton composition differs clearly between transitional water types. Some questions are raisedabout the Sado estuary, which behaves like a coastal lagoon for this element• Phytoplankton composition in transitional waters is potentially linked to water residence time. Thisshould be further explored, and if appropriate taken into account when establishing referenceconditions• Phytoplankton abundance may be adequately represented by biomass, using chlorophyll a as a proxy• Phytoplankton biomass and abundance should be assessed using an integrated methodology, becauseorganic enrichment effects may be manifested also in changes to benthic flora. The use of the ASSETSapproach, developed from the U.S. National Estuarine Eutrophication Assessment procedure isrecommended• Ecological status for fish is potentially best evaluated using Indices of Biotic Integrity (IBI)Pelagic reference conditionsA review was carried out of the approaches thatmay be used for determination of ecological qualitystatus in phytoplankton and fish, the latter qualityelement only for transitional waters. The relevanceof the various supporting quality elements wasalso analysed, using relationships developedfrom the TICOR databases and other sources.Benthic reference conditionsA review was carried out of the approaches thatmay be used for determination of ecologicalquality status of benthic quality elements, bothfor aquatic flora and fauna. A potential method forestablishing a scale for reference conditions ofbenthic plants based on relative areal distributionand biomass of opportunistic and long-livedspecies is outlined. The method needs to berefined and tested.The data collected on benthic macrofauna wereused extensively to explore a number of differentindices, across a range of transitional water types.v


Executive SummaryFigure 3. Application of indices as a function of data requirements and data availability.DATA AVAILABILITYQualitative dataQuantitative dataMetadataRough dataNumeric density dataNumeric density and biomass dataShannon-WienerShannon-WienerIdentification ofIdentification ofMargalefMargalefindividuals down toindividuals down toAMBIspecies levelfamily levelABCShannon-WienerMargalefMargalefAMBIABCFigure 3 shows a synthesis of the work carried out.A first generation approach to ecological qualitystatus may be carried out by using a combinationof appropriate indices, based on data availability.Special issuesTwo key areas were examined in the SpecialIssues chapter: Heavily Modified Water Bodiesand Pressure elements.One key finding of this part of the work is that there does not seem to be a basis for type differentiationof reference conditions for benthic fauna in transitional waters, in the application of the AMBI index andW-statistic. However, diversity indices may be regarded as type-specific, and will help to differentiatetypes in future developments of this method.For the first issue, TICOR results are based ondata developed by the relevant guidance group,defining the evaluation process that should befollowed for classification.The pressures guidance document was also usedas a framework for discussion of this issue, thefocus of the TICOR work is on the developmentof localised guidelines for the most relevantpressures on Portuguese transitional and coastalsystems.vi


IntroductionTHE WATER FRAMEWORK DIRECTIVEGeneral aspectsIn December 2000, as a result of a longprocess of discussion and negotiationbetween policy makers, experts and others,the Water Framework Directive (WFD) of theEuropean Commission was finally approved.This directive establishes a framework forcommunity action in what concerns water policyand management, and applies to all waters,including groundwater, inland surface water, andcoastal and transitional waters.Main objectives of the WFD• Prevent further deterioration of water resources, protecting and enhancing ecosystem status• Promote sustainable water use based on long-term protection of water resources• Enhance protection and improvement of the aquatic environment using specific measures in order toobtain a progressive reduction of discharges, emissions and losses of priority substances, as well asthe cessation or phasing out of discharges and emissions of priority hazardous substances• Ensure the progressive reduction and prevent further pollution of groundwater• Contribute to mitigate the effects of floods and droughtsPurpose of the WFD objectives• Assure the provision of water of good quality and quantity for human consumption as well as for theneeds of other socio-economic activities, in a sustainable manner• Protect territorial and marine waters, namely in what concerns elimination of sea water pollution• Achieve the objectives of relevant international agreements, including those which aim to prevent andeliminate pollution of the marine environment1


IntroductionAll this can be summarised in a key objective ofWFD: To achieve a good water status for allcommunity waters by the year 2015.Transitional and coastal watersThe WFD defines transitional waters as “bodiesof surface water in the vicinity of river mouthswhich are partly saline in character as a result oftheir proximity to coastal waters but which aresubstantially influenced by freshwater flows” andcoastal waters as “surface water on the landwardside of a line, every point of which is at a distanceof one nautical mile on the seaward side from thenearest point of the baseline from which thebreadth of territorial waters is measured,extending, where appropriate up to the outer limitof transitional waters”.All transitional and coastal waters have tobe classified in types, according to System Aor System B, as defined in Annex II of the WFD.System A• Mean annual salinity• Tidal range (transitional), depth (coastal)System B• Obligatory factors for transitional and coastalwaters: Latitude, longitude, tidal range andsalinity• Optional factors for transitional and coastalwaters: Current velocity, wave exposure, meanwater temperature, mixing characteristics,turbidity, mean substratum composition, watertemperature• Optional factors only for transitional waters:Depth, residence time and shape• Optional factors only for coastal waters:retention time of enclosed baysFor System A all the descriptors are pre-defined.System B establishes obligatory factors andsome optional factors. The number of typesfound using system B has to be equal toor greater than the number obtained usingsystem A.For each type of water characterised, typespecific conditions shall be established inaccordance with Annex V of the WFD, usinghydromorphological, physicochemical andbiological quality elements. Type specificreference conditions may be spatially based,based on modelling or may be derived using acombination of these methods. If it is not possibleto use these methods, Member States may useexpert judgement to establish such conditions,as is the case in the U.S. under EPA regulations.Member States have also to collect and maintaininformation on type and magnitude of thesignificant anthropogenic pressures to whichsurface water types are liable to be subject.2


IntroductionCOMMON UNDERSTANDING STRAGEGYReasons and objectivesThe implementation of the WFD raises challenges,which are widely shared by Member States. Thecomplexity of the text and the diversity of possiblesolutions to scientific, technical and practicalquestions, the extremely demanding timetable,incomplete technical and scientific basis, withsome fundamental issues in Annex II and V, whichneed further elaboration in order to make thetransition from principles and general definitions topractical implementation successful, and a strictlimitation of human and financial resources, areexamples of these challenges. That justifies thepreparation of a common strategy.Elements for a common strategy for the WFD• The need to share information between Member States and the European Commission• Information and involvement of the public, and public awareness on the implementation of WFD• The need to ensure coherence between the implementation of WFD and other sectorial and structuralpolicies• The need to ensure coherence between the implementation of WFD and other water directives• The need to integrate activities on different horizontal issues for the effective development of river basinmanagement plans and implementation of the WFD• The necessity for capacity building in Member States• The need to involve stakeholders and the civil society• The establishment of working groups and the development of informal guidance and supportdocumentsThe aim of this common strategy document is toallow a coherent and harmonious implementationof the WFD. Most of the challenges anddifficulties are inevitably common to all MemberStates, and many of the European river basins areshared, crossing administrative and territorialborders, where a common understanding andapproach is crucial to successful and effectiveimplementation.Emphasis is placed on methodological questionsrelated to a common understanding of thetechnical and scientific implications of the WFD.The aim is to develop supporting technical andscientific information to clarify and assist in thepractical implementation of the directive. Theguidance documents and recommendations foroperational methods produced for that purpose3


Introductionhave only an informal and non-legally bindingcharacter, and will be used by Member States ona voluntary basis.A modular structure has been chosen, themodules being the following key activities:Activity 1: information sharingActivity 2: development of guidance on technicalissuesActivity 3: information and data managementand reportingActivity 4: application, testing and validationWorking groups were created for the differentactivities, and their objectives, mandates,expected outcomes and timetables wereestablished.The first phase of the process is nowconcluded, and these working groups haveended their mandates. The guidancedocuments are now available and will betested in some river basins chosen by MemberStates, in order to identify any difficulties. ForPortugal, the choice was the Guadiana riverbasin.Working Groups Established in the First Phase of the Strategy• WG on the analysis of pressures and impacts• WG on designation of heavily modified waters• WG on classification and reference conditions of surface waters• WG on classification and reference conditions for coastal and transitional waters• WG on inter-calibration• WG on economic analysis• WG on monitoring• WG on assessment and classification of groundwater• WG on best practices in river basin management• WG to develop a shared geographical information system• WG on streamlining and reporting process4


IntroductionOBJECTIVESIn order to address these issues, the TICORproject was carried out. TICOR brought togetheran interdisciplinary team, for a period of one year,with the following objectives.• Develop an integrated approach for the application of the Water Framework Directive to all Portuguesecoastal and transitional waters• Provide the framework and methodology for classifying and delimiting Portuguese coastal andtransitional systems• Assemble the data required for WFD typology and first generation reference conditions, based on WFDcriteria and on the guidance provided by the Common Implementation Strategy working group COAST• Deliver a set of maps for typology of a key subset of Portuguese coastal and transitional waters• Derive a set of first generation reference conditions for Portuguese coastal and transitional types• Review the special issues of Heavily Modified Water Bodies and of Pressures and their application toPortuguese coastal and transitional watersKEY REFERENCESEuropean Community, 2000. Directive of theEuropean Parliament and of the Council2000/60/EC, establishing a Framework forCommunity Action in the Field of Water Policy. 62 p.Vincent, C., Heinrich, H., Edwards, A., Nygaard,K., Haythornthwaite, J., 2003. Guidance ontypology, classification and reference conditionsfor transitional and coastal waters. EuropeanCommission, report of CIS WG2.4 (COAST). 119 p.5


MethodologyThis chapter provides a brief overview of thedifferent initiatives and stages followed during theTICOR project life cycle.TICOR TEAM AND EXPERTISEThis work was carried out by nine team membersand four consultants, covering a wide range ofareas in marine science (Figure 4). A consultantfrom Northern Europe helped to provide a morebalanced approach to the work from an EU-wideperspective, and one from the U.S. FederalAgency NOAA allowed us to put this work into awider context, by taking into account theapproaches being followed in the EuropeanUnion and in the United States.Figure 4. Expertise, experience and professional areas of the TICOR team.PROFESSIONAL AREASEXPERIENCEEXPERTISEFundamental researchApplied researchWater basin managementFisheries managementRegulation and licensingImpact statementsConsultancyCruisesField workTaxonomyMesocosmsExperimentsDatabase managementMathematical modellingGeographic informationsystemsImpact assessmentMarine monitoringFish ecologyWater qualityEcological modellingCoastal eutrophicationXenobioticsBenthic ecologyHydrologyBasin managementFisheries managementRegulatory and licensingSTRUCTURE AND TIMINGThe TICOR workplan was divided into threeworkpackages, the first of which dealing withsystem definitions and data collection, and the7


Methodologysecond with typology and reference conditions.Workpackage three was concerned withcoordination, product delivery and dissemination.The project started on the World EnvironmentDay, 2002, and had a duration of one year.TICOR considered a meaningful subset ofPortuguese transitional and coastal waters (seeFigure 25) which together account for about100% of the area of transitional waters,corresponding to 9 estuaries, and 75% ofrestricted coastal waters. All the continental opencoastal area was included, but the coastal areasof the Azores and Madeira were explicitlyexcluded.Work packages, deliverables and productsThe list of tasks to be carried out for eachworkpackage is shown in Figure 5.Figure 5. TICOR workpackages and tasks.WorkpackageWP1System definition and historical dataWP2Typology and reference conditionsWP3CoordinationTasks1.1 Listing of systems and basic definitions1.2 Information for database loading1.3 GIS implementation1.4 Linking relational databases to GIS1.5 Web-driven database and metadatabase2.1 Application of WFD criteria for typology definitions2.2 First generation (G1) reference conditions2.3 Synthesis of reference conditions2.4 Artificial and heavily modified water bodies2.5 Special issues, designation of water bodies3.1 Coordination3.2 Product delivery3.3 DisseminationThe first task consisted of listing the systems andproviding the basic definitions for areal coverage,which effectively corresponds to an overallinventory. This allowed the project to be aware ofthe range of coastal and transitional systems inPortugal to which the WFD is applicable, whichwas an essential precondition for a comprehensivenational typology.TICOR was organised around monthly meetings ofthe project team, which were roughly split alongtwo workpackages, the first of which dealt withsystem definitions and data collection, and thesecond with typology and reference conditions.There were multiple challenges in accomplishingChallenges• Data availability and adequacy. Data collectionfor a wide diversity of systems highlighted theimbalance between different topics andsystems;• Use of a methodology matching the WFDrationale, for ecological status. The classicalapproach is focused on ecosystems ratherthan types;• Information flow and coherence betweenthematic areas;• Uncertainty regarding aspects of WFD guidancecurrently in progress.8


Methodologya programme of this nature in a period of oneyear, including data issues, integration andtransnational questions.The deliverables identified for the twoworkpackages are shown in Figure 6. Thesedeliverables were consolidated into four types ofproducts, designed to maximise the utility of thework carried out for the decision-makers andwater managers who must implement the WFD ata national level.Figure 6. Deliverables for each TICOR workpackage.WorkpackageWP1System definition and historical dataWP2Typology and reference conditionsDeliverables• Criteria for definition and division of systems• Website with systems and baseline information• GIS with zone identification and delimitation• Databases and web implementation• GIS for coastal zone with sampling stations• GIS for typology• First generation reference conditions• Synthesis of reference conditions for ecologicalquality ratiosThe final products of TICOR are:1. A digital set of raw data for all the TICORecosystems, which supported the work carriedout during the project, and forms the basis forthe historical dataset which will be developedupon by the different WFD monitoring initiativeswhich must now be implemented. This takes theform of ten different relational databases,distributed on the internet, and accompanyingsoftware for data entry, mining and output;2. A geographical information system for thetypology of Portuguese coastal and transitionalwaters;3. A minimum of three scientific papers publishedin peer-reviewed international journals, withthe objective of scientifically validating themethodologies explored or developed inTICOR;4. A book describing the objectives, approachand main outcomes of the project, designed toappeal to a broad technical readership.9


MethodologyPROJECT MANAGEMENTThe approach taken for project management isshown in Figure 7. Management was divided intothree key areas: team communication, datahandling and dissemination and documentproduction and delivery.The website developed for use over the projectlife-cycle acted as a hub for disseminatinginformation. Every project meeting included aseries of talks given by participants, based onwork carried out in the interim periods: the slidesand other materials from each of these wereFigure 7. Management approach for TICOR.COMMUNICATION DATA HANDLING DOCUMENTSBi-monthlyIdentify relevant dataWEBSITEExtended project teammeetings with INAGLocate data producersSchedulesAgendasMeeting minutesMonthlyTICOR projectteam meetingsDay to dayTICORWebsiteEmailPhoneP E R I O DOutsource data loadingand formatingPopulate databasesDistribute to TICOR teamDocument downloadsDocument uploadsLiteratureInternet linksREPORTSTexts in englishReview by consultantsImproved textsBook and scientific papersmade available on the website, and theinformation which was produced during thisprocess formed the backbone of the workpresented herein.Throughout the duration of the project, a series ofwatershed events were defined at differentworkshops – these were used to reachconsensus decisions on a range of concepts,methodologies and practical application issues.KEY REFERENCESAdams, J.L., 1986. Conceptual blockbusting, aguide to better ideas. Perseus books, 3 rd ed. 161 pp.Bentley, J., 2000. Programming pearls. Addison-Wesley. 239 pp.Brooks, F.P., 1995. The mythical man-month.Essays on software engineering. Addison-Wesley.322 pp.10


ToolsINTRODUCTION AND OBJECTIVESThis chapter reviews the tools used and developedin TICOR. The TICOR tools may be divided intothree categories based on their role in the project.OVERVIEW OF TOOLSRole in projectThe correspondence between the objectives to beachieved and the tools to be applied is presented inFigure 8.TICOR toolsData analysis toolsSupply the framework for the project as a whole.Typology toolsAre used to apply the criteria for type definition.Ecological status evaluation toolsProvide the methods to define first generationWFD reference conditions.Figure 8. Application of tools to each of the TICOR objectives.Tool appliedAllData analysis toolsTypology toolsEcological statusevaluation toolsNot applicableTICOR objectiveDevelop an integrated approach for the application of the Water FrameworkDirective to all Portuguese coastal and transitional watersProvide the framework and methodology for classifying and delimiting Portuguesecoastal and transitional systemsAssemble the data required for WFD typology and G1 reference conditions, basedon WFD criteria and on the guidance provided by the Common ImplementationStrategy Working Group COASTDeliver a set of maps for typology of a key subset of Portuguese coastal andtransitional watersDerive a set of first generation reference conditions for Portuguese coastal andtransitional typesReview the special issues of Heavily Modified Water Bodies and of Pressures andtheir application to Portuguese coastal and transitional waters11


ToolsBrief descriptionRelational databaseFor the relevant transitional and coastal water bodies relational databases were built for water qualitydata assimilation and management, using the Barcawin2000 TM software.Geographic information systemFor the analysis and management of spatially distributed data a geographical information system (GIS)was implemented for each water body.Typology toolsFor the application of the set of obligatory and optional factors defined under classification system B(WFD Annex II), in order to define the different types of transitional and coastal waters.Ecological status evaluation toolsThe aim of this toolset is to provide the means to evaluate the state of the water bodies. For each of thebiological quality elements in Annex V of the WFD, the methodology and metrics for ecological statusclassification were defined.DATA ANALYSIS TOOLSRelational databaseData assimilation was done using theBarcawin2000 software. For each system arelational database was built (Figure 9) except forthe Atlantic coast. The software in use has beendeveloped from 1985 onwards and has been usedby this team in multiple research projects withwidely varying data storage requirements.The main advantages of this database can besummed up as follows:• Organisation of information in a state-of-the-artrelational database;• Security for five levels of user access;• Easy input of data, by mapping MS-Excelspreadsheets to database fields, followed byautomatic import and validation;12


ToolsFigure 9. Number of stations, parameters, samples and results for TICOR system databases.System Stations Parameters Samples ResultsMinho estuary 18 34 322 3 538Lima estuary 31 70 603 8 096Douro estuary 39 42 292 5 006Ria de Aveiro 84 91 1 441 13 499Mondego estuary 48 290 726 18 317Tagus estuary 146 151 8 702 81 003Sado estuary 299 60 3 801 24 164Mira estuary 119 178 6 469 30 704Guadiana estuary 118 39 35 677 133 896Ria Formosa 70 165 97 021 139 932Totals 972 1 120 155 054 458 155Overall total 615 301• Numeric listings and search results are outputto an Excel compatible spreadsheet, or tographs created directly in Excel.Geographic information systemGIS was used to store and analyse spatial data.For each system a GIS was implemented basedon bathymetric data layers. The main propertiesof these layers are indicated in Figure 10.A schematic representation of a bathymetry layeris shown in Figure 11.For the data analysis and map production the GISFigure 10. Properties of bathymetric layers.Surface water Bathymetry Bathymetry coverage Conversion/body category System resolution (m) (% total area) Source type interpolationMinho 30 x 30 51% Irregular grid MCILima 5 x 5 72% Paper Digitisingbathymetric chartDouro 30 x 30 56% Irregular grid MCITransitional Ria de Aveiro 30 x 30 100% Irregular grid MCIwater Mondego 30 x 30 60% Irregular grid MCITagus 30 x 30 95% Irregular grid MCISado 30 x 30 80% Irregular grid MCIMira 30 x 30 22% Irregular grid MCIGuadiana 30 x 30 100% Irregular grid MCICoastal Atlantic Coast 50 x 50 100% Bathymetric Triangulationwater isolines (10 m)Ria Formosa 30 x 30 100% Irregular grid MCI* 1 MCI - Minimum curvature interpolation13


ToolsFigure 11. Bathymetry layer representation.Bathymetry sampleDepth scale (m)-5-203


Tools• The identification of the limit of saltwater intrusion,either on the basis of salinity observations or bydetermining the theoretical upper limit of netsaltwater exchange;• The selection of the method followed thedecision rule shown in Figure 12.The cross section upstream of which there is nonet exchange between salt and fresh water isFigure 12. Decision rule to identify upper limit of transitional water bodies.IFTidal weir orMorphological featureYESNOBathymetry, tidalelevations and dynamictide limitNODeterminefreshwater netexhangeSelect upper limitLongitudinal profilesof salinitydetermined as a function of the flow and tidalamplitudes and is designated as the theoreticalupper limit of net saltwater exchange. Themethodology is fully described in the chapterSystems, Limits and Morphology.Transitional water downstream limitsThe downstream limit is defined on the basis of:• Morphological / physical features such as a“barrier” (sand bar) with influence on waterexchange processes;• Conspicuous points defining a closure line;• Traditional limits established by the maritimeauthorities.Coastal water limitsThe coastal water limits were determined on thebasis of the WFD definition (Article 2.7):• The offshore limit is a line defined in the WFDby points “at a distance of one nautical mile onthe seaward side from the nearest point of thebaseline from which the breadth of territorialwaters is measured”;• The inshore limit is defined by the high waterlimit at maximum spring tide, except at theoffshore limit of transitional waters.Morphological parametersThe water volume and area were calculatedusing GIS techniques from the bathymetricdata, considering three situations for waterheight.• Zo (mean tide level at the tide gauge)• Equinoctial spring tide high water;• Equinoctial spring tide low water.15


Toolsbiomass, together with composition andabundance of other aquatic flora, and keysupporting elements such as dissolved oxygen.For fish, which were considered in the pelagicchapter, six indices were reviewed.CDI - Estuarine Community Degradation IndexBHI - Estuarine Biological Health IndexFHI - Estuarine Fish Health IndexEBI - Estuarine Biotic Integrity IndexFRI - Estuarine Fish Recruitment IndexFIR - Estuarine Fish Importance RatingThe EBI was selected as the most promisingmethod for assessing the quality status of fishcommunities. Detailed suggestions are made forthe application of EBI to Portuguese transitionalwaters, and a review of available data andrequirements was carried out.Benthic classification toolsThe benthic quality elements composition andabundance, as well as presence/absence ofdisturbance sensitive taxa, were evaluated withbiological indices.The selected indices integrate the qualityelements defined in the WFD. All of them havebeen applied to wide geographical areas and tozones disturbed by different types of pollution.This first generation of benthic referenceconditions / ecological classification tools is not• Shannon-Wiener index• Margalef index• AMBI Marine Biotic Index• ABC curves method, using the W-statisticstrictly type-specific. The AMBI index and theW-statistic are universal in terms of theirapplicability, i.e. the interpretation of measurementsis independent from the geographic area or thetype of system. However, diversity measures andtheir interpretation are strongly dependent onthe geographic variation and on the type ofsystem, in the sense that a value estimated usinga given diversity index does not have the samesignificance in warm temperate and borealsystems, or in an open coastal area and anestuary located at the same latitude. A decisionrule was developed for application of indicesas a function of data requirements and dataavailability (Figure 13).The description of the indices and the jointvaluation resulting from the combination of two orthree of them (depending on the type of dataavailable) is detailed in the Benthic ReferenceConditions chapter.Information on macrophytobenthos in Portuguesetransitional and coastal waters is scarce. This meansthat although macrophyte species composition andabundance can be found for some systems, thedynamics of macroalgae, seagrass and saltmarsh17


ToolsFigure 13. Benthic biological indices as a function of data availability.What type of available data?Qualitative dataQuantitative dataNumeric density and biomass dataNumeric Identification down Identification down toMetadata Rough data density data to species level family levelShannon-Wiener Shannon-Wiener Method ABC Shannon-WienerMargalef Margalef Margalef MargalefAMBI AMBI Method ABCvegetation is not well understood. For this reason itwas not possible to test the different approaches andto examine the possible associations betweenbiological descriptors and supporting elements in thePortuguese types. However some guidelines for theestablishment of reference conditions are presentedin the Benthic Reference Conditions chapter.KEY REFERENCESBilyard, G.R. 1987. The value of the benthic faunain marine pollution monitoring studies. Mar.Pollut. Bull. 18: 581-585.Buddemeier, R.W., Maxwell, B.A., 2000. Typology:Low-budget remote sensing. LOICZ NewsletterNº15, June 2000.Harrison, T.A., Cooper, J.A.G., Ramm, A.E.L., 2000.Geomorphology, ichthyofauna, water quality andaesthetics of South African estuaries. Dept.Environmental Affairs and Tourism, Pretoria,South Africa. ENV-DC 2000-01.Tett, P., Gilpin, L., Svendsen, H., Erlandsson, C.P.,Larsson, U., Kratzer, S., Fouilland, E., Janzen, C.,Lee, J., Grenz, C., Newton, A., Ferreira, J.G.,Fernandes, T., Scory, S., 2002. Eutrophication andsome European waters of restricted exchange.Continental Shelf Research, In 1630-1671.Warwick, R.M. & Clarke, K.R., 1994. Relearningthe ABC: taxonomic changes and abundance/biomass relationships in disturbed benthiccommunities. Mar. Biol.118: 739-744.Vogt, J., Peedell, S., Annoni, A., Paracchini, L.,Jager, A., Faber, W., Teunis, B., Ringeltaube, J.,Britton, P., Wirthmann, A., Thomas, R., 2003.Implementing the GIS elements of the waterframework directive. European Commission.Joint research center. WFD working group GIS.18


Systems, Limits and MorphologyINTRODUCTION AND OBJECTIVESThe WFD defines “transitional waters as: bodiesof water in the vicinity of river mouths, which arepartly saline in character as a result of theirproximity to coastal waters, but which aresubstantially influenced by freshwater flows”.Their delimitation has to take into considerationthis dual influence of fresh and coastal waters,which is translated into characteristic salinitygradients. The problem of establishing limits fortransitional waters derives from the fact thatthese gradients are variable as a function of acombination of factors, acting at different timescales, the more relevant being tidal situation andrange and fresh water flows.Nevertheless, there is a need to define geographicboundaries, since the application of the WFDimplies:• The calculation of morphological parameters(areas and volumes);• The identification of a spatial domain forapplication of:- Reference conditions- Environmental quality objectives• The design of monitoring programmes.METHODS AND CRITERIAReview of available approachesThe definition of transitional waters agreeswith the simple concept of “estuary” asproposed by Nelson-Smith. On the basisof this “fuzzy” definition it is difficult toestablish clear criteria to locate the boundariesof transitional waters. The most relevantcharacteristics of transitional waters are thecyclical variations of water level and salinity,which drive changes in other ecologicallyrelevant variables. For a variety of reasons,including administrative and historical ones,the estuary head or upstream limit has beenadopted as the limit of tidal influence. For thesea boundary the most common criterion isthe open coast line. These options havelimited practical use in the context of the WFD,since the limit of transitional waters must berelated to salinity values. At the head ofthe estuary, the tide may be advecting freshwater, and for large river flows, the influence offresh water in the coastal salinity may benoticeable. For practical reasons, we haveadopted a definition of the seaward limit basedon the identification of a limiting section, asother options based on salinity distributionsin the immediate coastal vicinity presentfeasibility issues.19


Systems, Limits and MorphologyTheoretical basisThe proposed methodology for the identificationof the upstream boundary of transitional waters isbased on concepts derived from simplifiedmixing models of estuarine circulation and salinitydistribution.Figure 14. Schematic representation of the estuarine circulation.SEA 35 30 25 15 10 5 0 RIVER SEA RIVERIn a typical estuary, the mixing of fresh andsalt water is not complete, due to the buoyancyof the less dense fresh water tending to float sothat there is a vertical gradient of salinity as wellas a longitudinal one. The net circulation of theestuary, over a sufficiently large number of tidalcycles, is established in such a way that amovement of saltwater upstream balances theseaward movement of freshwater. Schematicallythe “equilibrium circulation” is illustrated inFigure 14. The slope of the salinity isolinesshows the degree of vertical stratification.the river flow contributes all the water required tofill the intertidal volume. Thus, the water abovethis section should be completely fresh. On theebb tide there is a net loss through this crosssection of a volume of fresh water equal tothe volume introduced by the river during atidal cycle.It should be noted that this is a dynamic ratherthan a geographical boundary and implies thatthe head of the estuary moves upstream anddownstream with changes in river flow and tidalrange.The concept of the limit of net exchange ofsaltwaterThe schematic presentation of the circulation ofestuaries leads to the concept of “limit ofsaltwater exchange”. Early studies on this type ofwater bodies address the theoretical basis of thisconcept and propose a methodology for itsdetermination.A transitional water body is a region wherethe mixture of seawater and freshwater ismeasurable: therefore its inner end can bedefined as the cross section above whichthe volume which raises the water level from lowtide to high tide is totally contributed by the riverflow. On the flood tide there will be no netexchange of water through this section as20


Systems, Limits and MorphologyThe method to determine this section wasdeveloped in studies of estuarine flushing. It usesa segmentation technique: on theoretical groundsthe full validity of this implies that a steady stateis observed when there is a net seaward transportover a tidal cycle of a volume of fresh water equalto the volume introduced by the river in the sameperiod. When such a steady state cannot beassumed to occur, the method is not valid. Forpractical reasons, this limitation is not consideredin this study, which means that the assumptionsof the methodology may not be completely met inall the systems.Advantages of the proposed definitionThe proposed definition for the upper limit oftransitional waters has clear advantages. It isconceptually simple and has a clear physicalmeaning. It has no intrinsic difficulty of applicationand requires simple data on morphology andtidal elevations. Nevertheless, it is the availabilityof simple data, identified below, that createsthe main difficulties for the application of themethod.Data requirementsThe determination of upstream limits of transitionalwaters requires information on:• Location of dynamic tidal limit. This limit is oftendefined by using the discharge curve to establishthe end of the influence of tidal elevation orthrough local anecdotal evidence.• Morphology of upper reaches. Most bathymetricdata is obtained for navigational purposes. Thismay exclude upper reaches, although crosssectionsare commonly available for the tidalfresh water zones. Shoreline elevation andshape are also needed.• Tidal elevations in the upper reaches.• Freshwater flows over a section representingthe discharge into the system.METHODSUpstream limitsThe proposed methodology adopts as the upperlimit of the transitional waters a cross section21


Systems, Limits and Morphologyupstream of which there is no net exchangebetween salt and fresh water for a pre-defined flow.This section is established using a stepwiseprocedure (Figure 15):1. Determine the dynamic upstream tidalpropagation limit A. This can be done either byconsidering this limit to be an appropriate weir,or in cases where a weir does not exist, byexamining the water height records.2. Calculate the total volume B discharged by theriver during a tidal cycle T. Guidance: The modalflow as published by INAG is adopted here inas the reference river flow Q.3. Determine what equivalent length L of theestuary downstream of A is required to fit thevolume B (above low water level). Data on theestuarine bathymetry and local tidal elevationsare required for this.4. The downstream limit C is the estuary limit atthe head.5. The cross section C is determined by plottingthe cumulative volume upstream of consecutivesections against a linear dimension (thedistance to the limit of dynamic tidepropagation), and entering the dischargevolume on that curve.Practical questionsThe application of this methodology to the TICORsystems revealed some difficulties:• Uncertainty regarding the dynamic tide limit,coupled with contradictory information in theavailable literature;• Morphology of the upper reaches not easilyavailable, incomplete and/or outdated;• No information on tidal elevations in the upperreaches.Alternative approachesWhen data availability difficulties do not allow theapplication of this methodology, it may be stillpossible to apply alternative models to estimatelongitudinal salinity distributions.When neither of these alternatives is possible, thedefinition of the upper limit has to rely on heuristicapproaches e.g. information on water uses withsalinity requirements.Figure 15. Schematic representation of the estuary.B=Q TALBC22


Systems, Limits and MorphologyDownstream limitsThe methodology for identifying downstreamlimits of transitional waters relies on a combinedapproach, which is based on morphologicalfeatures and historical or traditional seawardlimits.Particular morphological features such assandbars or other barriers influencing the freeexchange of seawater with estuarine brackishwater were identified, and a survey of thejurisdiction of local maritime and port authoritieswas carried out. The limit lines were identified andrepresented in appropriately scaled maps: theyare generally associated with lines defined byconspicuous points (landmarks) and reflect a“traditional” knowledge of limits of characteristicphysical parameters.Other possibilities were analysed, such as theidentification of salinity gradients, but this is notfeasible in most of the systems, becausemeasurements of longitudinal salinity profiles arenot commonly available and the lack of adequatemorphological and tidal data did not allow theapplication of models to simulate suchlongitudinal distributions.The different approaches given above werecombined to obtain the proposed delimitation.SYSTEM SELECTION METHODOLOGYAccording to the WFD Guidance on the CommonUnderstanding of Terms - Part B, a minimum areaof 1 km 2 is recommended for consideration oftransitional waters. On this basis, not onlytransitional waters but also coastal waters suchas lagoons were identified according to thefollowing approach:1. Listing of all Portuguese rivers, estuaries andcoastal lagoons shown on 1:25000 militarycharts;2. Classification of these systems according tosize classes:Class A: < 0.3 km 2 ;Class B: ≥ 0.3 to < 0.7 km 2 ;Class C: ≥ 0.7 to < 1.0 km 2 ;Class D: ≥ 1.0 km 2 ;3. Selection of the TICOR systems from the classD list;4. Characterisation of the TICOR systems usingarea, volume, freshwater discharge, salinity,tidal range, tidal prism and limits as the maindescriptors.23


Systems, Limits and MorphologyFigure 16. Relative number of transitionaland coastal systems in each size class.D)36%RESULTSC)7% B)5%A)52%From a total of 44 systems identified astransitional or coastal, about half of them areclassified within class A (≤ 0.3 km 2 ) systems. Theother 48% are distributed over the other classes.Class D (≥ 1.0 km 2 ) is the most representative ofthese (Figure 16).Figure 17 presents the total list of Portuguesetransitional and coastal systems according tosize classes, including minor estuaries, estuaries,coastal lagoons and artificial structures (portsand marinas). Class A is mainly composed ofminor estuaries and class D of estuaries.Intermediate classes B and C have fewersystems, consisting mainly of artificial structuresand coastal lagoons.The system area, resident population, economicand ecological importance and geographicallocation were the main factors considered inFigure 17. List of the Portuguese transitional and coastal systems according to size classes.≥ 0.3 to≥ 0.7 toTypes of systems < 0.3 km 2 < 0.7 km 2 < 1.0 km 2 ≥ 1.0 km 2Minor estuaries Ancora, Cabanas, Lis, - - -Alcobaça, Alcabrichel,Sorraia, Sizandro, Safarujo,Cuco, Lisandro, Colares,Manique, Parreiras,Fontainhas, Odeceixe,Aljezur, Bordeira, Bensafrim,Alcantarilha, Quarteira,AlamoEstuaries Neiva, Ave - Cávado Minho, Lima, Douro,Ria de Aveiro, Mondego,Tagus, Sado, Mira,Arade, GuadianaCoastal lagoons - Melides S. Martinho Ria de Alvor, Riado Porto Formosa, Sto. André,Albufeira, ÓbidosArtificial structures - Vilamoura Port of Póvoa Port of LeixõesMarina de Varzim (Leça estuary)Total number of systems 23 2 3 16Overall total 4424


Systems, Limits and Morphologyselecting the TICOR systems. The followingsystems were chosen from class D: Minho, Lima,Douro, Ria de Aveiro, Mondego, Tagus, Sado,Mira, Ria Formosa and Guadiana (Figure 25).Figure 18. Points that identify the straightbaseline (D.L. nº 495/85).COASTAL LIMITSThe coastal water limits were determined on thebasis of the WFD definition (Article 2 (7)) forcoastal waters: “…surface water on the landwardside of a line every point of which is at a distanceof one nautical mile on the seaward side from thenearest point of the baseline from which thebreadth of territorial waters is measured”.The national legislation regarding the baselinefrom which the breadth of territorial waters ismeasured is D.L. nº 495/85, which was previouslydefined by D.L. nº 47771 (Figure 18). The linebetween points is the baseline defined by pointsin D.L 495/85 (green circles in Figure 18). Thebaseline boundaries at the NW and SE limitsfollow the tidal datum contour.0 50 kmCoastal waterdepth (m)03080150>150For the inshore limit the maximum spring highwater mark was considered. Figure 19 shows thelimits for the Atlantic coastal waters consideringone nautical mile from the straight baseline to theinshore limit.Figure 19. Atlantic coast limits.APPLICATION TO TICOR SYSTEMSThe application to TICOR systems is shown inFigure 20 and Figure 21.MORPHOLOGICAL PARAMETERSMethodsFor each system, the surface area and watervolume were calculated using the bathymetrygrid stored in the GIS. The area was calculatedby multiplying the total number of grid cellsby the cell area. The water volume wasdetermined by multiplying the water heightof each prismatic element (Figure 22) by the0 50 kmCoastal waterdepth (m)03080150>15025


Systems, Limits and MorphologyFigure 20. Transitional system limits (only TICOR systems shown).Depth (m)> -5-303> 5LimitsNNo data 0 4000 ma) Minho estuary.Depth (m)> -5-303N0 2000 m> 5LimitsNo datab) Lima estuary.Depth (m)> -5-30N0 2000 m3> 5LimitsNo datac) Douro estuary.26


Systems, Limits and MorphologyFigure 20. (cont.) Transitional system limits (only TICOR systems shown).Depth (m)> -5-303N0 2000 m> 5LimitsNo datad) Mondego estuary.N0 4000 mDepth (m)> -5-303> 5LimitsN0 8000 mNo dataDepth (m)> -5-3f) Tagus estuary.03> 5LimitsNo datae) Ria de Aveiro.27


Systems, Limits and MorphologyFigure 20. (cont.) Transitional system limits (only TICOR systems shown).N0 4000 mDepth (m)> -5-303> 5LimitsNo datag) Sado estuary.N0 4000 mNDepth (m)> -5-303> 5LimitsNo data0 2000 mh) Mira estuary.Depth (m)> -5-303> 5LimitsNo datai) Guadiana estuary.28


Systems, Limits and MorphologyFigure 21. Limits for coastal systems.a) North Atlantic coast.Coastal waterdepth (m)030800 50 km150>150b) Ria Formosa.N0 4000 kmDepth (m)> -5-303> 5LimitsNo data29


Systems, Limits and MorphologyFigure 22. Volume calculation based on the bathymetry.Cells within tidal height#1 #2 #3 #4 #5 #6Bottom levelSurface levelTidal height XMean sea level 0Excluded cellsWater depthPrismatic elementDepth (m)cell area and then integrating for the wholesystem.Three tidal situations were considered for thearea and volume calculations:• Z o (mean tide level at the tide gauge reference);• Equinoctial spring tide high water;• Equinoctial spring tide low water.The same tidal height was used for the wholesystem: different surface heights due to delays intidal propagation were not considered.Areas and volumes per systemFigure 23 shows the calculated areas andvolumes for each system using the WFD criteria.KEY REFERENCESCaspers H., 1967. Estuaries: Analysis of Definitionsand Biological Considerations In: Estuaries. Lauff,G. H. (Ed). American Association for the Advance ofScience, nº 83, Washington. D. C.Dyer, K. R., Taylor, P. A., 1973. A simplesegmented prism model of tidal mixing in wellmixed estuaries. Estuarine and Coastal MarineScience, Vol. 1, pp. 411-418Fairbridge, R. W., 1980. The Estuary: its definition30


Systems, Limits and MorphologyFigure 23. Areas and volumes for all TICOR systems.Area (km 2 ) Volume (10 6 m 3 )System name High water Z0 Low water High water Z0 Low waterMinho estuary* 23 23 21 105 67 38Lima estuary* 6 5 5 24 19 15Douro estuary* 6 6 6 83 65 49Ria de Aveiro 74 60 16 184 84 39Mondego estuary* 11 9 6 35 21 10Tagus estuary* 340 330 230 2 800 2 200 1 700Sado estuary* 180 160 120 1 060 770 550Mira estuary* 3 3 3 18 17 16Guadiana estuary 21 18 17 135 96 74Ria Formosa 91 49 19 210 92 45Atlantic coast 8 400 518 500* - Systems with incomplete bathymetry on the upstream part. Parameters were calculated based on mean estimates of channel structure.Note: Different colours correspond to different types.and geodynamic cycle. In: Chemistry andBiogeochemistry of Estuaries, E. Olausson & I.Cato, (Eds.) pp1-35. Interscience Publication.John Wiley and Sons. New York.Ketchum, B. H., 1955. The Exchange of Freshand Salt Waters in Tidal Estuaries. Journal ofMarine Research, 10, 1, pp18-37.Nelson-Smith, A., 1978. Estuaries – Basic physicaland ecological features. In: The Coastline. R. S. K.Barnes (Ed). John Wiley and Sons. New York.31


TypologyINTRODUCTION AND OBJECTIVESThe definition of water body types is one of thefirst stages in the implementation of the WaterFramework Directive, as outlined in Annex II. Theaim of typology is to separate surface waters intowater types in order to produce a simple physicalcharacterisation, ecologically relevant andpractical to implement. This process should befinalised in the year 2004 (Article 5 (1)). Thetypology is intended as a tool to assist the overallpurpose of the Water Framework Directiveestablished in article 1: the protection of bothwater quality and water resources preventingfurther deterioration and promoting theimprovement of the aquatic environment.Limitations for number of typesSurveillance Monitoring is one of the nationalobligations established in the Water FrameworkDirective concerning the reference conditionsdefined for each transitional and coastal type. Inthe WFD there is no guidance on the specificnumber of types each Member State must have.However, a large number of types will result in arequirement for a large number of type-specificreference conditions. Furthermore, the costs ofmonitoring a large number of types should alsobe taken into account. Although it is recognisedthat a simple typology system will need to becomplemented with a more sensitive referencecondition framework, a smaller number of typeswill be more amenable to management.WFD Typology elementsIn Annex II of the WFD, the differentiation withinthe transitional or coastal waters should be madeaccording to type. Types may be defined usingeither “system A”, which identifies types accordingto a fixed typology or “system B”, an alternativetypology based on physical and chemical factorsthat determine the characteristics of thetransitional water and hence the biologicalpopulation structure and composition. Typologydefined under system A consists of identifyinggeographical ecoregions and using (a) meanannual salinity and tidal range classes tocharacterise transitional waters or (b) meanannual salinity and depth classes to characterisecoastal waters. The alternative system Bcharacterisation uses both obligatory andoptional factors, as shown in Figure 24.The Guidance for Typology in Transitional andCoastal Waters suggests the use of system B,building on a consensus of the EU MemberStates, and refers that each country should usethose obligatory and optional factors that aremost applicable to their own ecological context.33


TypologyFigure 24. Typology according to system A and system B.DescriptorsSystem A - Fixed Typology Transitional waters Coastal watersEcoregion Baltic sea Baltic seaBarents SeaBarents SeaNorwegian seaNorwegian seaNorth SeaNorth SeaNorth Atlantic OceanNorth Atlantic OceanMediterranean SeaMediterranean SeaTypeBased on mean annual salinity Based on mean annual salinity< 0.5 psu Freshwater < 0.5 psu Freshwater0.5 to < 5 psu Oligohaline 0.5 to < 5 psu Oligohaline5 to < 18 psu Mesohaline 5 to < 18 psu Mesohaline18 to < 30 psu Polyhaline 18 to < 30 psu Polyhaline30 to < 40 psu Euhaline 30 to < 40 psu EuhalineBased on mean tidal range Based on mean depth< 2 m Microtidal Shallow waters: < 30 m2 to 4 m Mesotidal Intermediate: 30 to 200 m> 4 m Macrotidal Deep: > 200 mSystem B – Alternative Characterisation Transitional waters Coastal watersObligatory factors Latitude LatitudeLongitudeLongitudeTidal RangeTidal RangeSalinitySalinityOptional factors Current velocity Current velocityWave exposureWave exposureMean water temperature Mean water temperatureMixing characteristics Mixing characteristicsTurbidityTurbidityMean substratum composition Mean substratum compositionWater temperature range Water temperature rangeResidence timeRetention time (of enclosed bays)DepthShapeNote: Adapted from the Annex II in the Water Framework Directive text.34


TypologyContext for Portuguese watersAbout 50% of Portugal’s border is with theAtlantic Ocean. Transitional waters, or estuaries,are distributed along the coast, a number of themwith an area greater then 1 km 2 .Coastal Portuguese waters include semienclosedand shallow lagoons located mainly inthe southern part of the country, and opencoastal waters, oriented North-South and East-West (Algarve coast). Coastal systems cover anarea about fourteen times greater thantransitional systems.Studies on transitional and coastal Portuguesewaters have been made over the last fourdecades. Although several spatial and temporaldata gaps were detected, particularly in coastalwaters, the information necessary to identifytypes has been assembled. Expert knowledgeand metadata were used as a complement to rawdata.Objectives and approachThe main objectives of this chapter are:• To describe the methodologies used for typologydefinition;• To present the final typology for transitional andcoastal Portuguese waters, including thedescription of each type;• To classify the transitional and coastal Portuguesesystems into types.Figure 25. Main coastal and transitionalPortuguese systems.MinhoLimaRia de AveiroMondegoÓbidos lagoonTagusAlbufeira lagoonMiraLeçaDouroSadoSto. André lagoonGuadianaRia de AlvorRia FormosaAradeTICOR systemsS P A I N0 25 50 kmMETHODSTwo main tools were used in the typing processof transitional and coastal Portuguese waters: atop-down approach, based on expert knowledge,and a bottom-up approach developed as a followupto the LoiczView clustering tool developed byLOICZ, and entitled “Deluxe Integrated Systemfor Clustering Operations” (DISCO), which iscurrently being used for clustering transitionaland coastal waters in the United States.Top-down approachIn the top-down approach, systems larger than 1km 2 were grouped into types based on a commoncharacterisation for obligatory and optional factors.The classification of transitional and coastalPortuguese waters was made using system B(Figure 24). This classification was found to bethe most appropriate for defining national typessince the biological composition and communitystructure usually depends on more descriptors35


Typologythan those listed in System A (Figure 24). Prior totyping, the identification of the Ecoregion forPortuguese transitional and coastal waters wasmade using map B from Annex 11 of the WFD.Based on the “Guidance for Typology inTransitional and Coastal Waters” the obligatoryfactors for systems larger than 1 km 2 wereselected. The same approach was made for theoptional factors suggested in the guidancedocument (Figure 26).Figure 26. Classification system and optional factors used for the typology of transitional andcoastal Portuguese waters.Category System of classification Obligatory factors Optional factors used for typologyTransitional waters B Latitude Mixing characteristicsLongitudeSalinityTidal rangeCoastal waters B Latitude Wave exposureLongitudeSalinityTidal rangeShapeDepthThe systems were then grouped into types basedon a common description. A preliminary typologylist was intensively reviewed and discussed bythe national experts and international consultantsand a final list was then approved by consensus.Bottom-up approachThe bottom-up strategy was made by means ofthe DISCO on-line clustering tool. This systemuses a web-based interface and has beendeveloped from the LoiczView package. An ASCIIfile was prepared containing available data onsystem B obligatory and optional factors (Figure26), which describe each of the transitional andcoastal Portuguese systems, and uploaded toDISCO. The number of clusters was set to thesame number of types defined in the top-downstrategy and a number of K-means clusteranalyses were performed, each considering acombination of the relevant variables.The names of the variables used in each DISCOrun are given in Figure 27. Run 3 includes allobligatory and optional factors considered in the36


TypologyFigure 27. DISCO clustering process for transitional and coastal Portuguese types.VariablesRun number Obligatory factors Optional factors1 • Latitude • Depth• Median salinity2 • Latitude • Depth• Median salinity• Shape (volume and area)3 • Latitude • Depth• Median salinity• Shape (volume and area)• Mixing characteristics (estuary number 1 )1Modular flow (m 3 d -1 ) / Normalized tidal prism (m 3 d -1 )top-down approach both for transitional andcoastal types, excluding longitude and tidalrange. Longitude-based clusters provide apotentially artificial division, and tidal range isuniform throughout the Portuguese coast and istherefore not a suitable type discriminant.RESULTS AND JUSTIFICATIONNational typology for transitional andcoastal watersAccording to map B of WFD Annex XI, thetransitional and coastal Portuguese waters fallwithin the Atlantic Ocean Ecoregion, which isincluded in the Atlantic / North Sea Ecoregioncomplex proposed in the WFD guidance. ThePortuguese typology, defined using a top-downapproach, consists of seven types identified fromA1 to A7. The first two are types of transitionalwaters and types A3 to A7 belong to the coastalwaters category (Figure 28).coastal types are identified for open coastalwaters: Exposed Atlantic Coast, ModeratelyExposed Atlantic Coast and Sheltered AtlanticCoast. In the bottom-up typology, although RiaFormosa is discriminated from all the transitionalsystems, it is grouped with the Sheltered AtlanticCoast type. However, due to its specificcharacteristics (shallow enclosed coastal water) itmay be heuristically distinguished as a separatetype.The results obtained in the bottom-up approachare shown in Figure 29. In this analysis threedifferent types were recognized for coastalwaters and a further three for transitional waters.The results for the final DISCO run werecompared with the top-down typology in Figure30. In both typing methodologies, three different37


TypologyFigure 28. Results of the Portuguese typology for transitional and coastal waters using atop-down approach.Type Descriptor Obligatory factors Optional factorsTransitional watersA1 Mesotidal Latitude: 41º 50’ N to 41º 08’ N Mixing conditions:stratified Longitude: 08º 41’ W to 08º 53’ W StratifiedestuaryTidal range 1 : 3.5 m (Mesotidal)Salinity: Polyhaline (24)A2 Mesotidal well- Latitude: 40º 37’ N to 37º 09’ N Mixing conditions:mixed estuary Longitude: 08º 43’ W to 07º 23’ W Well-mixedwith irregular Tidal range: 3.3 to 3.8 m (Mesotidal)river discharge Salinity: Polyhaline (20)Coastal watersA3 Mesotidal semi- Latitude: 39º 26’ N to 38º 05’ N Shape: Semi-enclosedenclosed lagoon Longitude: 09º 13’ W to 08º 47’ W Depth: < 2mTidal range: 2 m (Mesotidal) 2Salinity: Mesohaline 3A4 Mesotidal shallow Latitude: 36º 58’ N to 37º 08’ N Depth: 2mlagoonLongitude: 07º 51’ W to 08º 37’ WTidal range: 3.4 m (Mesotidal)Salinity: Euhaline (35)A5 Mesotidal exposed Latitude: 41º 50’ N to 39º 21’ N Wave exposure:Atlantic coast Longitude: 08º 41’ W to 09º 24’ W exposedTidal range: 3.3 to 3.5 m (Mesotidal)Salinity: Euhaline (35)A6 Mesotidal Latitude: 39º 21’ N to 37º 04’ N Wave exposure:moderately exposed Longitude: 09º 24’ W to 08º 40’ W moderately exposedAtlantic coast Tidal range: 3.4 to 3.5 m (Mesotidal)Salinity: Euhaline (35)A7 Mesotidal sheltered Latitude: 37º 04’ N to 37º 11’ N Wave exposure:coast Longitude: 08º 40’ W to 07º 24’ W shelteredTidal range: 3.4 m (Mesotidal)1Mean Spring tidal range;Salinity: Euhaline (35)2During periods of free connection to the ocean;3Strongly influenced by occasional freshwater inputs and by cycles of temporary communication with the ocean.38


TypologyFigure 29. Results of the portuguese typology for transitional and coastal waters using theDISCO bottom-up approach.VariablesRun 1 Run 2 Run 3Types • Latitude • Latitude • Latitude• Median salinity • Median salinity • Median salinity• Depth • Depth • Depth• Shape (area, volume) • Shape (area, volume)• Mixing characteristics(estuary number)1 • Minho • Minho • Douro• Douro• Douro2 • Lima • Lima • Minho• Ria de Aveiro • Ria de Aveiro • Lima• Mondego • Mondego • Ria de Aveiro• Mondego3 • Tagus • Tagus • Tagus• Sado • Sado • Sado• Mira • Mira • Mira• Ria Formosa • Ria Formosa • Guadiana• Guadiana• Guadiana4 • Exposed Atlantic Coast • Exposed Atlantic Coast • Exposed Atlantic Coast5 • Moderately exposed • Moderately exposed • Moderately exposedAtlantic Coast Atlantic Coast Atlantic Coast6 • Sheltered Atlantic Coast • Sheltered Atlantic Coast • Sheltered Atlantic Coast• Ria FormosaIn the bottom-up approach the northern estuariesare distributed through two different types andseparated from the southern estuaries, whichintegrate the third transitional type.However, in the top-down approach only twomain types of transitional waters are identified.Since one of the bottom-up transitional typesonly includes one system, and since there is arequirement to optimise the number of types, itwas agreed that only two types should bedefined for transitional waters, as defined in thetop-down typology. The final typology fortransitional and coastal Portuguese waters ispresented in Figure 28 and is characterisedbelow.Characterisation of typesThe characterisation of transitional and coastalPortuguese types is briefly described below,taking into account the factors used for typedefinition and other relevant information.Transitional watersA1 – Mesotidal stratified estuaryThis type of estuary, located in the northern partof the country, is characterised by high riverflows over the whole year, which promote39


TypologyFigure 30. Comparison of the results obtained in both strategies used for Portuguese transitionaland coastal waters typology process.Top-Down typologyBottom-Up typology1 • Minho estuary • Douro estuary• Lima estuary• Douro estuary2 • Ria de Aveiro • Minho estuary• Mondego estuary• Lima estuary• Tagus estuary• Ria de Aveiro• Sado estuary• Mondego estuary• Mira estuary• Guadiana estuary3 • Ria Formosa • Tagus estuary• Sado estuary• Mira estuary• Guadiana estuary4 • Exposed Atlantic Coast • Exposed Atlantic Coast5 • Moderately exposed Atlantic Coast • Moderately exposed Atlantic Coast6 • Sheltered Atlantic Coast • Sheltered Atlantic Coast• Ria Formosa7 • Óbidos lagoon Not included in the typing process• Albufeira lagoondue to lack of data• Sto. André lagoonstratification of the water column inside theestuary. The mean tidal range is about 2 m andmean annual salinities are about 20. The Minho,Lima and Douro are examples of this type ofestuary.A2 – Mesotidal well-mixed estuary with irregularriver dischargeThe river flow of this estuarine type dependsstrongly on the season. Generally the torrentialriver discharge is due to intense rainfall during thewinter months. These estuaries are consideredwell-mixed during the whole year, withstratification being rare and occurring in specificsituations such as extreme flood events.Examples of this type of estuary are the Tagus,Sado and Guadiana.40


TypologyCoastal watersA3 – Mesotidal semi-enclosed lagoonLagoons of this type have a direct but intermittentconnection with the ocean, which is frequentlyclosed by a sand bar. Artificial opening occursmainly in the summer months. These systems areshallow, with a mean water depth less than 2 m.Salinity varies widely and is strongly influencedby evaporation, occasional freshwater inputs(precipitation and runoff) and by cycles of temporarycommunication with the sea. The tidal influence onthe lagoons is moderate and only occurs duringperiods of free connection with the ocean. Sanddunes cover the coastal and lagoon shores andextensive reed beds colonise wetland areas. SantoAndré and Albufeira are two examples for this type.A4 – Mesotidal shallow lagoonThe communication between the lagoon and thesea is permanent and occurs through several inletslocated along the system. The shallow depth,strong tidal currents and high water renewal makethis type of lagoon vertically well-mixed. The meanwater depth is about 2 m and salinity values arealways above 30 since the freshwater input can beconsidered negligible – in summer conditions thistype of system may become an inverse estuary.This type encompasses a complex of coastalseawater lagoons on sandy or muddy soils,extensive mudflats, sandbanks, sand dunesystems, salt marshes, wetlands and subtidalseagrass beds. Ria Formosa and Ria de Alvor arethe most significant examples in Portugal of thistype of lagoon.A5 – Mesotidal exposed Atlantic coastThe western coast from the northern border withSpain to Cape Carvoeiro is divided in two mainmorphological parts. The first one, extendingsouth from the northern border with Spain until 41ºNorth is mainly rocky and shallow with cliffsalternating with small beaches. From 41º Northto Cape Carvoeiro, beaches are the mainmorphological structures, interrupted only by CapeMondego. Tides are semidiurnal with a spring tidalrange of 3.8 m. This coastal type has high energyhydrodynamics and is struck by storms from theNorth Atlantic particularly from October to March.Dominant wave direction is West and Northwestwith some occurrences from Southwest. Mostfrequent wave periods are in the range of 8 to 12seconds and wave heights are in the range of 1 to3 m. Under storm conditions waves of 8 m heightand period exceeding 16 seconds may occur.At Leixões an extreme wave height of 14.6 m canoccur for a return period of 50 years.A6 – Mesotidal moderately exposed AtlanticcoastThe moderately exposed coast is typical of thecoastline from Cape Carvoeiro to Ponta daPiedade. Cliffs replace the beaches from CapeCarvoeiro to Cape Raso (Lisbon). From Cape Rasoto Sines, two irregular coastal sectors alternate withtwo sandy sectors. From Cape Sines to Ponta daPiedade, cliffs, interrupted by small beaches, are themain morphological structures. The wave energy isslightly more attenuated than in the northern part,although peak wave heights vary between 14 m fora return period of 100 years in the Tagus, and 16.7m at Sines for a return period of 50 years.41


TypologyA7 – Mesotidal sheltered Atlantic coastThis type stretches from Ponta da Piedade inthe western part of the Algarve to the Guadianaestuary, on the Southeastern border with Spain.From Ponta da Piedade to 8º West, cliffs interruptedby small beaches typically form the coast. Between8º West and 7º30’ West the main feature are thebarrier islands of the Ria Formosa (type A4).Following this lagoon system a coastal plain formedmainly by beaches extends until the Guadalquivirestuary in Spain. The southern coast has a milderwave climate than the western coast, with long andfrequent calm periods. Wave heights are seldomabove 4 m with means between 0.6 and 1.5 m. Wavedirection is from Southwest and Southeast andperiods are similar to those of the western coast.Typology applicationThe typology was applied to systems larger than1km 2 (Figure 31). Considering the number ofsystems per type, A2, mesotidal well-mixedestuaries with irregular river discharge, is themost representative for transitional waters andA3, semi-enclosed lagoons, is the mostrepresentative for coastal waters. Figure 32presents the location of each system identified bytype. A total area of 618 km 2 was calculated fortransitional waters while coastal systems,including open coast, cover an area fourteentimes larger, with 8464 km 2 .About 93% of the total area for transitional waters(644 km 2 ) is covered by systems of type A2. ForFigure 31. Classification of the transitional and coastal Portuguese waters according types.Category Type Systems larger than 1 km 2 Number of systemsTransitional waters A1 Minho estuary 4Lima estuaryDouro estuaryLeça estuaryA2 Ria de Aveiro 7Mondego estuaryTagus estuarySado estuaryMira estuaryArade estuaryGuadiana estuaryCoastal waters A3 Óbidos lagoon 3Albufeira lagoonSt. André lagoonA4 Ria de Alvor 2Ria FormosaA5 From Minho estuary 1until Cabo CarvoeiroA6 From Cabo Carvoeiro 1until Ponta da PiedadeA7 From Ponta da Piedade 1until Vila Real de Sto. António42


TypologyFigure 32. Location, areas and volumes of the transitional and coastal Portuguese types.MinhoMinhoLimaDouroRia de AveiroMondegoÓbidos lagoonS P A I NCape CarvoeiroS P A I NTagusAlbufeira lagoonSadoSto. André lagoonMiraGuadianaRia de AlvorRia FormosaAradeA1 A20 25 50 kmA3 A40 25 50 mlA5Ponta da PiedadeA6A7Vila Real deSto. António0 25 50 km0 25 50 mlTYPOLOGY OF TRANSITIONAL WATERS ANDSHELTERED COASTAL WATERSA1 A2 A3 A4Area High water 32 630 9 94(km 2 ) Mean sea level 32 586 55Low water 30 393 37Volume High water 170 4 242 18 400(10 6 m 3 ) Mean sea level 122 3 233 182Low water 85 2 457 89TYPOLOGY OF OPEN COASTAL WATERSA5 A6 A7Area (km 2 )* 3 200 4 200 1 000Volume 195 000 295 900 27 600(10 6 m 3 )** Only one value given since there are no appreciable differences due to tidal height.43


Typologycoastal systems type A5 is the mostrepresentative, covering about 46% of the totalarea. In terms of water volume per type, similarproportions were obtained for transitional andcoastal waters (Figure 32).KEY REFERENCESCosta, F.V., Gomes F.V., Ramos, F. S., Vicente, C.M. 1996. History of coastal engineering inPortugal. In History and Heritage of CoastalEngineering, N.C. Kraus (Ed.) ASCE.European Community, 2002. Guidance forTypology in Transitional and Coastal Waters.11 p.Ferreira, J.G., Simas, T., Nobre, A., Silva, M.C.,Schifferegger, K., & Lencart-Silva, J., 2003.Identification of Sensitive Areas and VulnerableZones In Transitional and Coastal PortugueseSystems. Application of the United StatesNational Estuarine Eutrophication Assessment tothe Minho, Lima, Douro, Ria de Aveiro, Mondego,Tagus, Sado, Mira, Ria Formosa and Guadianasystems. INAG/IMAR, 2003, 151 pp.Smith, C.A. & Maxwell, B.A., 2002. Deluxe IntegratedSystem for Clustering Operations (DISCO).http://narya.engin.swarthmore.edu/disco/OSPAR Comission 2000. Quality Status Report2000: Region IV - Bay of Biscay and IberianCoast. OSPAR Comission, London. 134 + xiii pp.44


Pelagic Reference ConditionsINTRODUCTION AND OBJECTIVESThe WFD defines (in Annex V) a number of qualityelements, used for determination of ecologicalstatus, which may be considered to be pelagic,i.e. associated with the water column.This chapter provides an overview of thoseelements, examines which metrics may best beused for their determination, and discussespossibilities for definition of type-specificreference conditions.Finally, some points are made regardingintegration of some of the biological qualityelements, with particular reference to issuesconcerning organic enrichment.Objectives• To collect and review available data;• To assess the adequacy of the phytoplankton classification tools;• To test and develop these tools in order to recommend the best techniques for establishing referenceconditions for pelagic quality elements;• To suggest some first-generation reference conditions, and make recommendations for future work.WFD pelagic quality elementsFigure 33 shows the pelagic quality elements fortransitional and coastal waters. The list isabridged from the WFD Annex V to contain onlythose elements relating to the water column.Biological and supporting elements associated tothe benthic environment are examined in the nextchapter.The key differences in quality elements betweentransitional and coastal waters are highlighted.The most important of these is the inclusion ofthe biological element Composition andabundance of fish fauna in transitional waters, butnot in coastal waters.Review of phytoplankton classification toolsA number of tools are available which maypotentially be used for establishing type-specificreference conditions and ecological status ofwater bodies for phytoplankton composition,abundance and biomass.45


Pelagic Reference ConditionsFigure 33. Pelagic quality elements for transitional and coastal waters.Transitional and coastal watersBiological elements • Composition, abundance and • Composition and abundance ofbiomass of phytoplankton (6 months) fish fauna (3 years)Hydromorphological Morphological conditions: Tidal regime:elements supporting • Depth variation (6 years) • Freshwater flowthe biological elements• Direction of dominant currents• Wave exposureChemical and General: Specific pollutants:physico-chemical elements 1. Transparency • Pollution by all prioritysupporting the biological 2. Thermal conditions (3 months) substances identified as beingelements 3. Oxygenation conditions (3 months) discharged into the body4. Salinity (3 months) of water (1 month)5. Nutrient conditions (3 months) • Pollution by other substancesidentified as being dischargedin significant quantities into thebody of water (3 months)Note: Elements which are only applicable to transitional waters are shown in blue, elements applicable only to coastal waters are shown in red.Where applicable, the sampling frequency indicated in the WFD Annex V is shown in brackets.Although all the phytoplankton components areconsidered together as one biological qualityelement, it is useful to consider individually thethree phytoplankton descriptors indicated in theWFD.There are a number of candidate methods forevaluating these three descriptors, althoughgenerally these tools focus on a sub-set of thethree and/or combine these with other descriptorsof ecosystem state. Based on the guidancedeveloped by the CIS 2.4 (COAST) group, and ona review of additional possibilities, a list of potentialapproaches is shown in Figure 34, together with anevaluation of their usefulness.The first two methods are integrated assessmentprocedures, which combine several WFD qualityelements to either provide a semi-quantitativescore (OSPAR) or a final calculation of state,known as overall eutrophic condition (NEEA/ASSETS). Both these approaches considerCompositionThe phytoplankton species which make up thecommunityAbundanceThe number of cells which exist in a samplingvolumeBiomassThe mass of phytoplankton which exists in asampling volumedifferent stages in the eutrophication process,which result in progressively more severeimpacts. Phytoplankton biomass is evaluatedusing chlorophyll a as a proxy, and combined withsome of the supporting elements indicated inFigure 33, such as dissolved oxygen.Both procedures extend the evaluation of quality46


Pelagic Reference Conditionselements that are considered individually in theWFD to address the effects of organic enrichmentin transitional and coastal waters (TCW) usinga more holistic approach. The effects ofnutrient discharges to TCW may result inelevated phytoplankton biomasses, changes inphytoplankton composition or modifications tothe phytobenthos, manifested through the shift incommunity structure from seagrasses and longlivedmacroalgae to rapid blooms of opportunisticseaweeds.A key difference between the two approaches liesin the use of nutrients as part of the assessment.NEEA/ASSETS uses nutrients only in thepressure part of the assessment, but not fordetermination of state. Although it is clear thathuman inputs of nutrients are the driver for thesymptoms of organic enrichment which mayoccur in the coastal zone, dissolved nitrogen orphosphorus in the water column are often difficultto relate to phytoplankton composition, abundanceand biomass. Moreover, the loading is moreimportant than the observed concentration,although in many instances a clear relationshipbetween nutrient loads and peak phytoplanktonbiomass is not observed.IFREMER has developed a method for examiningspecies composition (Figure 34) grouping speciesaccording to toxic events and organic enrichment.In the former case, a checklist of species isprovided, whereas in the latter all species areconsidered. In both cases, cell number per unitvolume is used as a descriptor, and high statusresults from lack of symptoms over a moving five-Figure 34. Methodologies addressing the biological quality element phytoplankton composition,abundance and biomass, in whole or in part.Method Description Positive NegativeOSPAR Symptoms-based approach Integrated Non-exclusive, includesComprehensive identifying direct and indirect “EU accepted” benthic componentsProcedure effects. Includes nutrients. such as seaweedsSemi-quantitative (+/- scale)Draft standard, not well testedNEEA/ASSETS Similar to above, identifying Integrated Non-exclusive, includesAssessment primary and secondary Quantitative benthic components suchof Estuarine symptoms. Contains Well tested as seaweedsTrophic elements of P-S-R. in U.S. “U.S.Status Excludes nutrients accepted”IFREMER Composition approach based One of very Not integratedtentative on: Toxic species (human, few approaches Eutrophication is betterclassification aquatic life) & Eutrophication to composition assessed with biomassspecies (all) over a moving5 year periodSouth African Multi-metric index based on Integrated Excludes chlorophyll but“state of suitability for aquatic life, Applied to 250 includes nutrientsthe estuaries” human contact & trophic status South Africanreportestuaries47


Pelagic Reference Conditions• High concentrations of suspended material intransitional waters may control light availabilityfor phytoplankton production• Phytoplankton blooms will not usually occur intransitional waters with a water residence timelower than the phytoplankton doubling timeyear period. Toxic blooms advected inshore fromocean frontal systems present a problem for thisclassification, since this type of event is apparentlyunrelated to land-based pressures. On the otherhand, eutrophication is probably better identifiedusing biomass rather than abundance, and maynot manifest itself at all in the phytoplankton.The South African State of the Estuaries reportdevelops an index for estuarine quality, whichdoes not include a phytoplankton component,and therefore appears to be of limited use for theWFD.Review of fish classification toolsThe WFD specifies that the descriptors thatshould be used for establishing type-specificreference conditions and ecological status ofwater bodies for fish fauna are the following:a) Fish assemblages and relative abundanceb) Relative abundance of sensitive speciesFish communities have often been used to illustratechanges in the condition of estuarine environments,despite the fact that these assemblages intransitional waters are usually dynamic.A review of the literature Figure 35 shows six typesof ecological indices that include the estuarinefish fauna component and may potentially beuseful for the application of the WFD.The first two methods are based on a comparisonbetween the fish community present within anaquatic system and the reference community.The Estuarine Community Degradation Index(CDI) assumes that differences between thepotential community and the present assemblageare due to habitat degradation. However thisapproach seems too simple because changes infish communities are not only due to habitatdegradation but also to pressures such asfisheries. Despite this, the CDI is a useful methodbecause it can be used to monitor the recovery of48


Pelagic Reference ConditionsFigure 35. Methodologies addressing the biological quality element fish fauna composition andrelative abundance.Method Description Positive Aspects Negative AspectsCDI Based on differences between a Condenses fish Only refers presence/absencefish community and a reference community of species without proportionsinformationBHI Based on similarities between a Condenses fish Only refers presence/absencefish community and a reference community of species without proportionsinformation uses two separate measuresFHI Qualitative and quantitative Comparison Simulation of the referencecomparisons with a reference between number conditions (mean value offish community of species each group)inclusion of exoticor translocatedspeciesEBI Set of a scoring system of fish Integrated with Difficulties in the establishmentmetrics using a reference representative of the scoring systemmetrics of fishcommunity statusFRI Use of ichthyological Biologically Lack of knowledge of someinformation to assess changes meaningful ecological factors affectingin habitat integrityfish communitiesFIR Set of a scoring system Identifies which Difficulties in the establishmentof criteria reflecting the systems have of the scoring systemimportance of estuaries to fish a high fishconservationpriorityCDI - Estuarine Community Degradation Index; BHI - Estuarine Biological Health Index; FHI - Estuarine Fish Health Index;EBI - Estuarine Biotic Integrity Index; FRI - Estuarine Fish Recruitment Index; FIR - Estuarine Fish Importance Ratinga system, to document its faunistic degradationover time and to support the identification oftypes where the fish communities are mostendangered.The Estuarine Biological Health Index (BHI) isderived from the CDI, and incorporates ameasure of the degree of similarity between thepotential community and the actual community(or present assemblage).Although the BHI has been an important tool incondensing information on fish assemblages intoa single numerical value, the index doesn’ttake into account the relative proportions ofspecies present but only their presence/absence.Furthermore, the BHI formula combines twoseparate measures (health and importance) into asingle index.The Estuarine Fish Health Index (FHI) is based onboth qualitative and quantitative comparisonswith a reference fish community. The qualitative49


Pelagic Reference Conditionsapproach uses the number of species within eachtransitional waterbody, whilst the quantitativeapproach is based on the relative abundance ofthe species. In both approaches, a comparison isthen made to the average number of species(qualitative) and percentage abundance of thespecies (quantitative) for the geomorphic groupto which each water body belongs.In qualitative and quantitative assessments,exotic and translocated fish species are includedin the fish assemblages for each estuary type, butare not considered in the reference condition.The Estuarine Biotic Integrity Index (EBI) reflectsthe relationship between anthropogenic alterationsin the ecosystem and the status of higher trophiclevels. The EBI includes the following eight metrics:• total number of species• dominance• fish abundance (number or biomass)• number of nursery species• number of estuarine spawning species• number of resident species• proportion of benthos associated species• proportion of abnormal or diseased fishThe usefulness of this index requires it toreflect not only the current status of fishcommunities but also be applicable over a widerange of estuaries, although this is not entirelyachieved.The Estuarine Fish Recruitment Index (FRI) wasdeveloped in an effort to use ichthyologicalinformation to assess changes in habitat integrity,especially the availability and suitability ofestuarine nursery areas to marine migratoryfishes. The FRI is a biologically meaningfulmanagement index, but the data requirementsare critical.The Estuarine Fish Importance Rating (FIR) isbased on a scoring system of seven criteria thatreflect the potential importance of estuaries to theassociated fish species. This index is able toprovide a ranking, based on the importance ofeach estuary and helps to identify the systemswith major importance for fish conservation.The indices described above condenseinformation about fish fauna communities into amore functional format, which can be used toplan and manage the aquatic systems. Thepresence/absence of sensitive species isinsufficient to determine the health of thecommunity, but their relative abundance or thereturn of important species (diadromous speciessuch as eel, shad and salmonids) could representan important indicator for the determination ofecological status of water bodies.METHODOLOGYPhytoplankton and supporting elementsData were collected for the three descriptors forthis biological element (i.e. biomass, abundance,composition), together with a number ofsupporting quality elements, including hydrologyand tides, water temperature and salinity,dissolved oxygen, nutrients, and some specificpollutants. The data cover the range of typesproposed for Portuguese transitional and coastalwaters, and usually span periods of several years.Several different approaches were tested on thedataset, to examine the possible associationsbetween biological descriptors and supportingelements. Some of the supporting elements, suchas tidal range, river discharge, current velocity andsalinity are part of the criteria for typology: thus, it50


Pelagic Reference Conditionsshould theoretically be possible to establish somequantitative relationships, since reference conditionsare considered to be type-specific.Species compositionThe dataset used in the analysis of speciescomposition spans over six decades, and coversall seven TCW types proposed for Portugal.Due to this fact, it is considered to be acomprehensive listing of the phytoplanktonspecies present, including those representative ofpristine conditions.Figure 36 shows a summary of this dataset,which was loaded in a relational database.Queries were used to (i) explore the number ofspecies common to all or some of the types; (ii)perform a principal components analysis (PCA) ofthe distribution across types; and (iii) extract datasubsets for comparison with supporting elementssuch as tidal range or freshwater discharge.Abundance and biomassA review of the available literature shows thatphytoplankton abundance is very often determinedFigure 36. Number of species in a range of systems covering all types.Type System Nº of species % of total speciesA1 Minho estuary 99 8.6A2 Mondego estuary 174 15.2A2 Tagus estuary 342 29.8A2 Sado estuary 416 36.3A2 Ria de Aveiro 293 25.5A3 Albufeira lagoon 200 17.4A3 Óbidos lagoon 403 35.1A3 S. Martinho do Porto bay 264 23.0A4 Ria Formosa 213 18.6A5 Minho until Cabo Carvoeiro 514 44.8A6 Cabo Carvoeiro until Ponta da Piedade 587 51.2A7 Ponta da Piedade until V. R. Sto António 394 34.4Total number of species 1 147Note: transitional waters in blue, coastal waters in green.51


Pelagic Reference ConditionsKey approaches• To review the possible relationships betweenabundance and biomass and selectedsupporting elements;• To determine the most suitable approach foran integrated assessment of ecological statusfor these descriptors.supporting elements which are associated to thebenthic environment are examined in the nextchapter. The WFD (Annex V) determines thattype-specific reference conditions based on thecomposition and abundance of fish fauna shouldbe established only in transitional waters.The WFD stipulates the following conditions forfish fauna at high quality status:by using biomass (i.e. chlorophyll a) as a proxy,due to the difficulty and cost of cell counts andbiovolume determination; Abundance andbiomass were therefore considered together.The analysis was focused on transitional watersand semi-enclosed coastal waters - InPortuguese coastal ecosystems there are few (ifany) concerns regarding these parameters inopen coastal waters.The following points were examined:• Relationship between winter maxima for dissolvedinorganic nitrogen and spring phytoplanktonblooms (expressed as chlorophyll a);• Relationship between turbidity and phytoplanktonbiomass;The use of the U.S. National Estuarine EutrophicationAssessment (NEEA) and Assessment of EstuarineTrophic Status (ASSETS) procedures as a means ofintegrating phytoplankton biomass and abundancewith relevant supporting quality elements.FishIn this chapter both pelagic and benthic speciesare discussed, despite the fact that biological andCompositionThe fish species which make up the communityAbundanceThe number of individuals which exist in asampling area• Species Composition and abundancecorrespond totally or nearly totally toundisturbed conditions,• All the type-specific disturbance-sensitivespecies are present.In Portugal, as in most of the European Union, thedefinition of type-specific reference conditionsbased on data from undisturbed sites is extremelydifficult, because such undisturbed types are rareor simply do not exist. Alternatively, somehistorical data and information concerning the fishfauna in specific sites may potentially be used toaccomplish this goal. That information may thenbe compared with present data. The use ofpredictive or hindcasting methods could also be auseful tool to define type-specific referenceconditions based on fish fauna, and will require aninterdisciplinary approach. Expert judgement israrely useful for quantitative assessment andtherefore it should be used only when the otheralternatives are not available, although it might bevaluable as additional information.The indices described previously condenseinformation about fish fauna communities into amore functional format, which may be used in themanagement process. The presence/absence ofsensitive species may not be sufficient to determinethe health of the community, but their relativeabundance or the recovery of important species(e.g. return of salmon to the Rhine) could represent52


Pelagic Reference Conditionsan important indicator on the determination of theecological status of water bodies.The various alternative methods described musttherefore be assessed to identify the most suitabletechniques for determining the ecological status ofPortuguese transitional waters.In this connection the development of anEstuarine Biotic Integrity Index based on fishcommunities could be useful for establishing theecological status of the Portuguese transitionalwater bodies (Figure 37). This index could provideadditional information on different quality aspectsand potential causes. The EBI could also behelpful to identify impacts and to plan moreefficient monitoring programmes. It is currentlyassumed that the first step in the development ofan EBI index consists in the selection ofappropriate metrics.In the second step, the scores of the metrics aregiven, through the comparison of the valuesobtained to expected values (referenceconditions). Following the original IBI metric,values approximating, deviating slightly from, ordeviating greatly from those at the reference sitesare scored as 5, 3, or 1, respectively. Finally, theFigure 37. Sequence of steps involved inthe application of the EBI.Data collectionSelection of the metricsReference data available?NOData collectionApply EBITotal EBI scoreScores obtained are as expected?NOModification of the metricsInterpretation of the resultYESYES53


Pelagic Reference Conditionsscores of the metrics in each system are added,to give a result ranging from 60, the maximumvalue – excellent; to 12, the minimum - very poor.Some of the problems associated to the creationof such an index are:1. Which metrics should be included and atwhat level (systems, types or national)?The selection of the appropriate metrics must bemade on the basis of the ecological relevance ofeach possible metric to fish community bioticintegrity, the most meaningful metrics beingselected. Metrics which vary clearly in thepresence of environmental stressors must beprioritized (e.g. sensitive species are the first todisappear when there is perturbation). Thesemetrics should be related to several aspects ofthe fish communities, such as species richnessand composition, trophic and reproductivecomposition, fish abundance and condition,among others. This implies the identification ofrelevant metrics among candidate metrics andpresumes the application of some sort ofdiscriminant analysis to previously collectedreference data.For the two Portuguese transitional water types,the selection of metrics should aim for a commonset. However, the type-specific classificationlevels will differ, due to the physical,hydrodynamic and biogeochemical differencesbetween types. The species which are sensitivein type A1 and A2 will quite probably differ, anddifferences in water temperature, freshwaterdischarge, stratification and water chemistry maylead to natural differences in dissolved oxygenconcentration, which even at saturation valuesnearing 100% may not be sufficient to allow thesurvival of certain salmonid species in type A2.2. In what way should the relative importanceof metrics be considered?The selection of appropriate metrics implies theidentification of relevant metrics among candidatemetrics. If the chosen metrics are not equallyimportant, then a weighting methodology shouldbe applied or some of its descriptors eliminated.Relative importance should be based on asignificant relationship with the environmentalstressors.3. How can reference conditions be obtainedin order to set the scoring criteria?Among all problems in the conception of the EBIindex, perhaps the most complex issue is theestablishment of type-specific reference conditions.The WFD considers multiple alternatives toaccomplish this goal, as discussed previously.Apart from the scarcity of historical data andinformation on systems (or types), transitionalwaters show high natural variability, which isdifficult to dissociate from anthropogenicdisturbance. Additionally, one of the mainsources of human disturbance, i.e. fisheries, isnot explicitly considered in the WFD.54


Pelagic Reference ConditionsThe establishment of type-specific referenceconditions using data from minimally-impairedsystems may considered as acceptable, as longas it applies to systems belonging to the sametype. It follows that this approach may only beused where such conditions exist. This is thecase for type A2, but not for type A1.4. How can the consistency of the results beguaranteed?In order to compare the results obtained with theindex in a system, through time, or between twodifferent systems, a consistent sampling design isrequired. This means that the sampling effort andgear have to be the same for all systems and, ingeneral, sampling effort should capture 90-95%of the species present at the site. This will alsoprevent the occurrence of bias due to differentsampling conditions.Finally, it seems that fish data analysis should beone component in a holistic approach, usinghydrographical, physical, chemical and complementarybiological data to interpret the results obtained.RESULTS AND DISCUSSIONPhytoplankton and supporting elementsSpecies compositionThe distribution of species across different types,grouped by major family, is shown in Figure 38.There is a clear difference between open coastalwater and waters with restricted exchange, bothcoastal and transitional. Open coastal types havea significantly lower percentage of diatoms, andprymnesiophytes are far better represented.Only 4% of species are common to all thesystems, corresponding to a total of 45, of which25 are diatoms and 16 are dinoflagellates. Theanalysis of the similarity of species compositionwithin a type could only be carried out for twotypes (A2 and A3), where data exist for multiplesystems. Figure 39 shows that the percentage ofcommon phytoplankton species for each typevaries between 20-50% for A2 and 30-70% forA3. It would therefore be reasonable to propose alist of species that should generally be present inwater bodies belonging to each of these types.Figure 38. Composition with respect to type.Lowest % diatomsHighest % PrymnesiophytesP. Piedade until V. R. Sto AntónioCabo Carvoeiro until Ponta da PiedadeFrom Minho until Cabo CarvoeiroRia FormosaRia deAveiroLagoa de AlbufeiraS. Martinho do PortoLagoa de ÓbidosSadoTejoMondegoMinho0% 20% 40% 60% 80% 100%Note: Open coastal water is shown in blue.55


Pelagic Reference ConditionsFigure 39. Species common to all systems of a type. Only data for types A2 and A3 are available.Type System Nº of species % of common species for typeA2 Mondego estuary 174 52A2 Tagus estuary 342 26A2 Sado estuary 416 22A2 Ria de Aveiro 293 31A3 Albufeira lagoon 200 67A3 Óbidos lagoon 403 33A3 S. Martinho do Porto bay 264 5168 species are common to both types A2 and A3,corresponding respectively to 75% and 50% ofthe total of species common to these types.Figure 40 shows the results of a principalcomponents analysis (PCA) performed on thenumber of species from four of the thirteenphytoplankton families, using all the availablesystems.The PCA shows a clear separation between thedifferent types. Open coastal types A5, A6 andA7 are in the top right quadrant, coastal lagoontypes A3 and A4 are in the left half of the figure,and transitional type A2 is in the lower part. TypeA1 data are available only for the Minho, whichis at the far left, but the Mondego, althoughclassified in type A2 shows similarities to typeA1, probably due to the low water residencetime. In type A3, Óbidos lagoon does not appearto fit well with other systems, perhaps due tothe fact that it is closed to the ocean for partof the year.An analysis was made of the possible relationbetween water residence time and number ofspecies present in each system.Figure 40. Principal components analysis for species composition, using diatoms, dinoflagellates,chlorophytes and prymnesiophytes.A1A4MondegoA380604020A7A5A6Diatoms-150 -100 -50 50 100 150 200-20-40L. ÓbidosKeyDinoflagellatesChlorophytesPrymnesiophytes-60-80-100-120-140Other familiesA256


Pelagic Reference ConditionsThis analysis was considered to be relevant onlyfor transitional waters, since in open coastalsystems the combined forcing of tidal exchangeand freshwater inputs is not applicable.Figure 41 shows that there is a clear relationbetween the two variables for a dataset whichincludes estuaries from both types A1 and A2,and which cover the whole of Portugal from north(Minho) to South (Guadiana).Water residence time in transitional watersintegrates both the river inflow and tidalexchange, thus implicitly taking into account theFigure 41. Number of phytoplankton species as a function of water residence time, for sixtransitional water systems, from two different types (A1 and A2).Number of phytoplankton species500450400350300250200150100500y = 14.79x + 122.6r = 0.93p < 0.01TagusSadoR. AveiroMondegoGuadianaMinhoSpecies data: 1929-19980 5 10 15 20 25Water residence time (days)Figure 42. Scheme for defining the number of species that should be present at varying degreesof ecological status.Number of phytoplankton species500450400350300250200150100HighGoodModeratePoor5000 5 10 15 20 25BadWater residence time (days)57


Pelagic Reference ConditionsWFD supporting elements salinity and freshwaterdischarge. Tidal range, which is one of thedescriptors for typology, is also included.The ecological status classification for phytoplanktoncomposition can therefore potentially be approachedin two ways.• A type-specific list for key species may be defined based on existing data. Reference conditions andEcological Quality Ratio (EQR) thresholds may be established on a presence/absence basis. Thesystem may be refined by further categorising groups of species and using weighting schemes to arriveat overall indices• For transitional water types, the number of species which should be present can be derived accordingto residence time, as shown in Figure 41, and EQR thresholds may be established using the type ofapproach illustrated in Figure 42Abundance and biomassThe application of the NEEA/ASSETS methodologyto the evaluation of the phytoplankton abundanceand biomass components allows the integrationof the pelagic chlorophyll a metric with someimportant benthic descriptors of organicenrichment such as opportunistic macroalgaeand alterations in submerged aquatic vegetation.Additionally, the supporting element dissolvedoxygen is included as a secondary symptom ofenrichment, but other supporting elements listedin Figure 33 are not. Salinity and temperature arestandard baseline parameters in transitional andcoastal waters, but they are not phytoplanktonindicators. Both salinity and temperature affectspecies composition, and temperature is aforcing function for primary production, but theseparameters are not “manageable” at a localscale, and exhibit high natural variability.Transparency is a supporting element shown tohave a direct association with phytoplanktonbiomass and abundance in freshwater systemssuch as lakes or reservoirs, and in microtidalsystems such as the Baltic Sea. However, inmesotidal transitional waters, the turbidity (andthus the transparency of the water column) islargely determined by erosion-depositionprocesses forced by the spring-neap cycle,58


Pelagic Reference ConditionsFigure 43. Chlorophyll a and suspended particulate matter (transparency proxy) for the Tagusestuary, a type A2 transitional water. 943 datapoints for surface samples taken over severalyears across the whole salinity range.Chlorophyll a (µg L -1 )504540353025201510500 50 100 1501098765432100 10 20 30 40 50Suspended particulate matter (mg L -1 )Note: The right-hand image zooms into the rectangular area on the left-hand image.which is associated to variable bed shear stressand vertical mixing dynamics. Figure 43 shows agraph for the Tagus estuary, a type A2 transitionalwater: there is no dependence of watertransparency on chlorophyll a; in mesotidaltransitional and sheltered coastal waters inPortugal, this supporting element clearly has ahigh natural variability (sensu WFD) and thereforeshould be excluded from the assessment ofecological status.The issue of the supporting element nutrientconditions, here interpreted to be nutrient(dissolved inorganic nitrogen and phosphorus)concentrations in the water column is particularlydifficult. Although the relationship betweendissolved nutrients (particularly phosphate) andphytoplankton blooms is well established infreshwater systems such as lakes, there is agrowing body of evidence that both the nutrientloading and the concentration of dissolvednutrients in transitional waters is often difficult torelate to pelagic algal biomass. Data gathered for59


Pelagic Reference Conditionsa range of European systems is shown in Figure44, using only dissolved inorganic nitrogen. In thesystems shown, nitrogen dominates as thelimiting nutrient for primary production. This is awell established pattern in many transitional andcoastal systems, where the dissolved nitrogen tophosporus ratio is often below 16 (in atoms).Figure 44 reveals that there is no clearrelationship between phytoplankton and nutrientconcentrations, for a broad range of EuropeanFigure 44. Maximum spring phytoplankton as a function of maximum winter dissolvedinorganic nitrogen (DIN).Maximum spring phytoplankton (µg chl a L -1 )302520151050GullmarenTagusGolfe de FosHimmelfjarden (inner)Himmelfjarden (outer)Clyde (main basin)SadoMondegoFirth of the Clyde (inner)KongsfjordenRia FormosaMiraGuadianaRia de AveiroMinhoDouroChlorophyll a estimated graphicallyNitrate instead of DIN0 50 100 150 200 250 300Maximum winter DIN (µM)Note: Percentile 90 for all data is used for the Portuguese systems, systems in green are from the EU OAERRE project, systems in blue are from TICOR.transitional and coastal waters, suggesting thenutrients are not a good indicator forphytoplankton ecological status as regardsabundance and biomass. The systems showninclude estuaries, broad and narrow fjords, riasand lagoons. There are a number of reasons forthe lack of association of nutrient concentrationand phytoplankton biomass:• Light availability may often be the limiting factor for pelagic primary production in turbid systems, whilstnutrients play a subsidiary role• Strong pelagic-benthic coupling may mean that a top-down control of phytoplankton biomass existse.g. due to bivalve filter feeding. This has been documented for estuaries such as S. Francisco Bay andcoastal systems such as the Ria Formosa. Physical factors such as water column depth and verticalstratification may thus play a key role in the development of pelagic algal blooms• Short water residence times do not allow the development of autochtonous phytoplankton blooms.Nutrient enrichment may lead instead to blooms of benthic algae such as Ulva or Enteromorpha, andto changes in seagrass communities60


Pelagic Reference ConditionsThis is the basis for the exclusion of this elementfrom the state component of the NEEA/ASSETSmethod, and is supported in a recent study byIFREMER on eutrophication in European waters.Studies carried out on the relationship betweennutrient loading and phytoplankton biomass in anumber of coastal systems are also inconclusive.It is recommended that the supporting elementnutrient conditions should be measured and usedfor monitoring pressure, and to explore therelationship between changes in nutrient ratios inthe water bodies and species shifts, with a focuson the appearance of nuisance and/or harmfulalgae, but not as a supporting element forphytoplankton abundance and biomass.The NEEA/ASSETS methodology (Figure 45) isenvisaged to be the most suitable for assessingthe ecological status for phytoplankton abundanceand biomass, and the supporting quality elementdissolved oxygen. Dissolved oxygen is used inNEEA/ASSETS as an indicator of advanced(secondary) symptoms of organic enrichment,following from enhanced chlorophyll a concentrations(pelagic or benthic). The inclusion of phytobenthicFigure 45. NEEA/ASSETS - Overall level of eutrophic condition. Recommended as anintegrated approach for the WFD biological elements of phytoplankton and phytobenthos.Overall level of expression of eutrophic conditions1High primarysymptomsMODERATEPrimary symptoms highbut problems with moreserious secondarysymptoms still not beingexpressedMODERATE HIGHPrimary symptoms highand substantial secondarysymptoms becomingmore expressed,indicating potentiallyserious problemsHIGHHigh primary symptomsand secondary symptomlevels indicate seriouseutrophication problems0.6Moderate primarysymptomsMODERATE LOWPrimary symptomsbeginning to indicatepossible problems but stillMODERATELevel of expressionof eutrophic conditionsHIGHSubstantial levels ofeutrophic conditionsoccurring with secondaryvery few secondaryis substantialsymptoms indicatingsymptoms expressedserious problems0.3MODERATE LOWMODERATE HIGHLow primarysymptomsLOWLevel of expressionof eutrophic conditionsModerate secondarysymptoms indicatesubstantial eutrophicconditions, but low primaryHigh secondarysymptoms indicateserious problems, but lowprimary symptomsis minimalsymptoms indicate otherindicate other factors mayfactors may be involved inalso be involved incausing the conditionscausing conditions0Low secondarysymptoms0.3 0.6 1Moderate secondarysymptomsHigh secondarysymptoms61


Pelagic Reference ConditionsFishApplication of the EBI to Portuguese transitionalwatersThe application of EBI to define referenceconditions for the two Portuguese transitionaltypes will draw on both historical data and onsystems which are presently undisturbed, orslightly disturbed. The historical data available forsome Portuguese systems is shown in Figure 46.components permits a fuller analysis of the rangeof potential eutrophication effects, which coupledto NEEA and ASSETS’s quantitative approach andspatial and temporal discretisation make this apowerful tool for examining the WFD phytoplanktonand phytobenthos biological quality elements.However, NEEA/ASSETS currently use fixedranges for pelagic chlorophyll a concentrationsand for dissolved oxygen, which potentially fallshort of a WFD requirement for type-specificreference conditions. This may be adapted ifrequired e.g. by defining chlorophyll rangesvarying with type, or by using percentagesaturation of oxygen to “localise” oxygen datawith respect to salinity and temperature.It appears that some historical data existconcerning fish abundance and distribution forsome systems of type A2, which would enablethe application of an EBI index. However, thesampling conditions used to obtain thosedatasets have to be considered and reproducedin future data collection.For the A2 systems, the Mira Estuary can beregarded as a relatively pristine estuary. The lackof information from this system must be resolvedthrough the collection of missing data, the type ofinformation depending on the metrics selected. Ingeneral, the metrics used rely on speciesrichness, composition and condition, as referred.On the other hand, for the systems whichintegrate type A1 it seems that there is nominimally impaired system suitable for use as areference, although some historical data on fishabundance and distribution for the Douro estuaryFigure 46. Historical data for fish available to establish reference conditions for Portuguesesystems.CompositionPresence ofTypes Systems (species list) Abundance Distribution sensitive speciesA1 Minho estuary 26 taxa Unknown Unknown YesDouro estuary Unknown Unknown Yes UnknownA2 Ria de Aveiro Yes Yes Yes YesTagus estuary > 100 taxa Yes Yes YesSado estuary Yes Yes Yes YesMira estuary Yes Yes Yes YesGuadiana estuary > 28 taxa Yes Yes Yes62


Pelagic Reference Conditionsmay be useful. Since type A1 may well be transnational,and occur also in Galicia in Spain, or inother Northeast Atlantic areas such as the Irishwest coast, it is possible that a relativelyundisturbed system outside Portugal may beused to establish reference conditions.Additionally, there are historical data (fishabundance and distribution) for the Douroestuary, which may be suitable. As mentionedpreviously, care must be taken to normalisepresent and future sampling procedures whencomparing with historical datasets.Although historical data (species lists) exist inPortugal for some systems, in the majority of casesthere is no information on community dynamics(number of individuals, biomass, etc), as well as onother descriptors such as dominance, proportionof benthic-associated species, or proportion ofabnormal or diseased fish, which rules out theapplication of EBI to these datasets.additionally covers some of the benthic floracomponents. Thresholds for reference conditionsshould be type-specific, normalised in some casesby the use of fixed ranges, which account fordifferences between types. The best example isthe use of dissolved oxygen expressed aspercentage saturation, which reflects salinity andtemperature differences between types.The reference conditions for species compositionmay be based on an extensive historical dataset,taking into account the effects of water residencetime on species number for transitional waters, asdiscussed previously.FishA number of approaches simpler than the EBIindex might be applied, as a first step, toPortuguese transitional waters in order to getsome classification of their ecological quality inthe framework of the WFD.Supporting elementsThere are a number of supporting elements whichshould be included in a definition of referenceconditions for fish, of which the most importantare abiotic factors such as dissolved oxygen,sediment organic content and bottom substratemodifications, and biotic factors such as theoccurrence of harmful algal blooms. Although inthe WFD no reference is made to the effects offishing, it should be recognised that in transitionalwaters the main pressures which contribute tosubstrate changes are channel dredging andbottom trawling.CONCLUSIONSPhytoplanktonA review of the potential approaches for evaluatingthe phytoplankton quality elements suggests thatthe biomass and abundance components shouldbe integrated with selected supporting elementsby means of the NEEA/ASSETS approach, which63


Pelagic Reference ConditionsIt is proposed that an investigative monitoringprogramme be put in place at selected systems,in order to apply an Estuarine Biotic Integrityindex, analyse the suitability of the metrics andclassification system, and make the necessaryadaptations.Such a program should last over a period of oneyear, synoptically in two systems, (e.g. the Minhoestuary for type A1 and the Mira estuary for typeA2). It should be followed by surveys of completionin other systems, which will allow the applicationof the metrics adopted and respective descriptorsto the whole set of Portuguese transitional waters.KEY REFERENCESBricker S.B., Clement C.G., Pirhalla D.E., OrlandoS.P., Farrow D.R.G., 1999. National EstuarineEutrophication Assessment. Effects of NutrientEnrichment in the Nation’s Estuaries, NOAA –NOS Special Projects Office, 1999.Bricker, S.B., Ferreira, J.G. & Simas, T., 2003. AnIntegrated Methodology for Assessment ofEstuarine Trophic Status. Ecological Modelling,169(1), 39-60.Cloern, 2001. Our evolving conceptual model ofthe coastal eutrophication problem. Mar. Ecol.Prog. Ser. 210:223-253.Deegan, L. A., Finn, J. T., Ayvazian, S. G., Ryder-Kieffer, C. A. & Buonaccorsi, J., 1997.Development and validation of an EstuarineBiotic Integrity Index. Estuaries 20, 601–617.Fano, E.A., Mistri, M., & Rossi, R., 2003. Theecofunctional quality index (EQI): a new tool forassessing lagoonal ecosystem impairment. Est.Coast. Shelf Science, 56, 709–716.Harrison, T.A., Cooper, J.A.G., Ramm, A.E.L.,2000. Geomorphology, ichthyofauna, waterquality and aesthetics of South African estuaries.Dept. Environmental Affairs and Tourism,Pretoria, South Africa. ENV-DC 2000-01.Ménesguen, A, 2001. L’eutrophisation des eauxmarines et saumâtres en Europe, en particulieren France. Rapport IFREMER DEL/EC/01.02 toEuropean Commission D.G. Env. B1. January2001.Moita, M.T., Vilarinho, M.G., 1999. Checklist ofphytoplankton species off Portugal: 70 yearsof studies. Portugaliae Acta Biol. Ser. B, Sist. 18:5-50.Whitfield, A.K., Elliot, M., 2002. Fishes asindicators of environmental and ecologicalchanges within estuaries: a review of progressand some suggestions for the future. Journal ofFish Biology, 61 (A), 229–250.64


Benthic Reference ConditionsINTRODUCTION AND OBJECTIVESThis chapter provides an overview of the benthicquality elements, tests different benthicclassification tools, and suggests the besttechniques for establishing benthic referenceconditionsObjectives• To collect and review available data for benthic aquatic flora;• To collect and review available data for benthic invertebrate fauna;• To describe and discuss the benthic aquatic flora and benthic invertebrate classification tools;• To present guidelines to establish reference conditions for benthic aquatic flora and benthic invertebratefauna and recommendations for future work.WFD benthic aquatic flora quality elementsIn Annex V of the WFD, the biological elementsreferred as typical flora of transitional andcoastal waters are divided into two maingroups: phytoplankton, which belongs to thepelagic category and is discussed in theprevious chapter, and “other aquatic flora”,which includes all the phytobenthic groups:microphytobenthos, macroalgae, seagrassesand saltmarsh vegetation. However, WFD AnnexV indicates only ecological status definitions formacroalgae and angiosperms in the section on“other aquatic flora”. These two groups aregenerally the most used in the evaluation ofanthropogenic influence on transitional andcoastal systems. For these reasons the furtherdiscussion on “other aquatic flora” refers tomacroalgae and angiosperms, including seagrassesand saltmarshes. Figure 47 presents the WFDquality elements related to aquatic flora intransitional and coastal waters.Review of benthic aquatic flora classificationtoolsA number of tools focusing on composition andabundance have been developed to establish thetype-specific reference conditions and theecological status of the aquatic flora. These toolsevaluate the aquatic flora considering theequilibrium between macroalgae and angiospermsaccording to the quality status of the65


Benthic Reference ConditionsFigure 47. Benthic aquatic flora quality elements for transitional and coastal waters.Transitional and coastal watersBiological elementComposition and abundance of Macroalgae and AngiospermsSupporting Morphological conditions: Tidal regime:hydro-morphological 1. Depth variation • Freshwater flowelements 2. Quantity structure and substrate • Direction of dominant currentsof the bed• Wave exposure3. Structure of the intertidal zoneSupporting chemical General: Specific pollutants:and physico-chemical 1. Transparency • Pollution by all priorityelements 2. Thermal conditions (3 months) substances identified as being3. Oxygenation conditions (3 months) discharged into the body4. Salinity (3 months) of water (1 month)5. Nutrient conditions (3 months) • Pollution by other substancesidentified as being dischargedin significant quantities into thebody of water (3 months)Note: Elements which are only applicable to transitional waters are shown in blue, elements applicable only to coastal waters are shown in red.Where applicable, the sampling frequency indicated in the WFD Annex V is shown in brackets.CompositionThe macroalgae and angiosperm species whichmake up the communityAbundanceThe coverage of macroalgae and density ofangiosperms which exist in a sampling areaenvironment. The rationale behind these methodscan be summarised in the following assumptions:• Angiosperms are mostly perennial species fromlate successional stages with low growth rates,long life cycles, and thus typical of consolidatedecosystems in a steady-state equilibrium• Angiosperms, particularly the submergedaquatic species, are very sensitive to disturbedconditions such as decreases in watertransparency, low oxygen conditions andorganic enrichment• In disturbed ecosystems angiosperms aregradually replaced by opportunistic specieswith high growth rates and short life cyclessuch as green algae and phytoplanktonFigure 48 presents the potential approaches aswell as comments on their usefulness. Thedescription of the first two methods as well as themain key differences between them is brieflypresented in the “Pelagic Reference Conditions”chapter.Although both procedures extend the qualityelements evaluation by means of a holisticapproach the individual assessment is alsoaddressed. The OSPAR Comprehensive Procedureexamines the shifts from long-lived to short-livednuisance species (e.g. Ulva sp.). In theNEEA/ASSETS approach, macroalgal conditionsare evaluated in terms of problematic growthfrequency (episodic or periodic blooms), whilesubmerged aquatic vegetation (angiosperms) is66


Benthic Reference Conditionsclassified according to the magnitude of losswithin the system.The Swedish tool uses three substrate-specificclassifications (soft-bottom, moderately exposedhard-bottom and exposed hard-bottom), accordingto the aquatic flora communities. Speciescomposition and abundance is examined in fivelevels of deviation (little or none, moderate,significant, serious and eradication) from thepristine natural conditions assessed by historicaldata. This method was developed for coastalwaters and still needs further testing.IFREMER has developed a method for examiningthe eutrophication stages of aquatic floracommunities assuming that, over an eutrophicationgradient, perennial species decrease in density andbiomass as the opportunistic species take over.Five quality status classes are establishedaccording to the degree of human impact, from asituation where there is no significant impact ofFigure 48. Methodologies addressing the biological quality element other aquatic floracomposition and abundance, in whole or in part.Method Description Positive NegativeOSPAR Analyse seagrasses and Integrated Non-exclusive, includesComprehensive seaweeds in terms of coverage “EU accepted” pelagic components such asProcedure and depth of occurrence and phytoplanktonmicro-phytobenthos biomassDoes not consider saltmarshesSemi-quantitative (+/- scale)Draft standard, not well testedNEEA/ASSETS Submerged aquatic vegetation Integrated Non-exclusive, includesAssessment of examined in terms of spatial Quantitative pelagic components such asEstuarine coverage losses Well tested phytoplanktonTrophic Macroalgae examined in terms in U.S. Does not consider saltmarshesStatus of bloom frequency and spatial “U.S. accepted”coverageSwedish Classification of the shore Adapted to the Only for coastal areasclassification communities in five levels of WFD levels of Not well testedtool for species abundance and classificationangiosperms compositionand rocky shorecommunitiesIFREMER Classification in five stages Integrated Not well testedEutrophication according to the oxygen Adapted to thestages conditions and species WFD levels ofcomposition and abundance classificationEcological Quantification of the relative Semi-quantitative Not well testedEvaluation species abundanceIndex (EEI) (opportunistic and latesuccessionals)67


Benthic Reference Conditionsuniform permanent polygons (well-definedsystems e.g. coastal lagoons) or lines (opencoast) the mean spatial coverage of each ESG isdetermined. The overall EEI is then achievedusing a heuristic set of categories, whichcorresponds to the levels of the WFD ecologicalstatus (high, good, moderate, poor and bad). Thismethod has been tested only on Greek coastaland transitional waters.Guidelines for the definition of referenceconditionsData on the Portuguese type-specific aquaticflora in transitional and coastal waters are scarce.Although composition and abundance of aquaticflora species can be found for some systems,the dynamics of macroalgae, seagrasses andsaltmarsh vegetation are not well known. For thisreason it was not possible to test the differentapproaches and to examine the possibleassociations between biological descriptors andsupporting elements in the Portuguese types.However some guidelines for the establishmentof reference conditions are presented.human activities to a strong eutrophic conditionwhen degradation of quality standards for aquaticflora and supporting elements decline due tohuman pressures. This is a semi-quantitativeapproach based on mapping data for macrophytesand sediments (organic matter distribution,nutrient concentrations). A quantitative developmentof this method is needed in order to improve theassessment.The Ecological Evaluation Index (EEI), developedin Greece, quantifies the shifts in the structure ofbenthic macrophytes considering two EcologicalState Groups (ESG): ESG I, which includes thosegenera with low growth rates and long life cycles(late successionals) and ESG II, which iscomposed of genera with high growth rates andshort life cycles. After the division of the area intoSpecies compositionA comprehensive listing of the aquatic floraspecies present in Portuguese transitional andcoastal types is needed. This list should identify,wherever possible, the historical presence ofFigure 49. Distribution of aquatic floragroups within transitional and coastalPortuguese types.Types Macroalgae Seagrasses SaltmarshA1 X X XA2 X X XA3 X X XA4 X X -A5 X - -A6 X - -A7 X - -X indicates presence; - indicates absence.68


Benthic Reference Conditionsperennial species as well as hydro-morphologicaland physico-chemical conditions, which effectivelysupport those communities. Some of thestandard baseline supporting elements, such astemperature, salinity and transparency, shouldnot be used for this purpose due to their highnatural variability, for reasons indicated in the“pelagic reference conditions” chapter.The current data on aquatic flora identify threemain groups for which reference conditionsshould be defined: macroalgae, seagrasses(including, when present, submerged angiospermsof the genera Ruppia, Potamogeton and Chara)and saltmarsh vegetation. Figure 49 shows thepresence of these groups within the Portuguesetypes.Species abundanceThe percentage of macrophytobenthos loss orovergrowth in terms of colonised area can beused as a type-specific reference condition forspecies abundance. This could be addressedcrossing historical and current data on the area ofmacrophytobenthos colonisation in order tocalculate the percentage changes in the colonisedarea, using GIS. A heuristic set of categories forthe percentage of loss / overgrowth can then bedefined in order to assess the ecological status.An integrated method based on the IFREMERand NEEA/ASSETS approaches is proposed inFigure 50 for long-lived and opportunisticmacrophytes. In this approach the information forlong-lived species is crossed with that foropportunistic macrophytes. An overall level forecological status is then determined. It must bestressed that this method does not take intoaccount saltmarsh vegetation.Also, the application of the NEEA/ASSETSmethodology for the evaluation of the abundanceof macroalgae and submerged aquatic vegetationallows the integration of these components withthe pelagic descriptors for phytoplankton.Dissolved oxygen is the only supporting elementincluded in the analysis as a secondary symptomof organic enrichment.69


Benthic Reference ConditionsFigure 50. Integrated method to evaluate the ecological status of long life and opportunisticmacrophyte species.1.0BAD POOR MODERATE GOOD HIGHHIGH0.8Long life speciesColonized area / Potential colonised area0.60.4GOODMODERATEPOOR0.2BAD0.01.0 1.8 0.6 0.4 0.2 0.0Colonised area / Potential colonised area of long life speciesOpportunistic speciesNote: Ecological status levels: blue for high, green for good, yellow for moderate, orange for poor and red for bad.WFD benthic invertebrate fauna qualityelementsFigure 51 shows the biological and supportingelements that are associated to the benthicinvertebrate fauna. Unlike those associated topelagic environment, here all the elements relatedto the water column and sediment are taken intoaccount, since one of the characteristics of thebenthic communities is their ability to integrateeverything that happens in the environment.Benthic communities can be considered moreadequate than those of the pelagic domain whenevaluating the status of the ecosystem. Due totheir limited mobility, they are more sensitive tolocal disturbance, and because of theirpermanence over seasonal time scales, theyintegrate the recent history of disturbances whichmight not be detected in the water column.Review of benthic invertebrate faunaclassification toolsAmong the biological quality elements for the70


Benthic Reference ConditionsThe WFD establishes as pristine situations forthe benthic communities in transitional andcoastal waters those in which the diversity andabundance of invertebrate taxa is within therange normally associated with undisturbedconditions. Also, all the disturbance sensitivetaxa associated with undisturbed conditionsshould be present.WFD ecological status definitions are thecomposition and abundance of benthic invertebratefauna.Species composition and abundance of benthicorganisms can be integrated in the formulation ofbiological indices, facilitating the task of themanagers when interpreting the response of thesystem towards a specific impact on theenvironment.Among the numerous indices found in thebibliography, there are different approaches inusing each one of them when evaluating thestatus of a system. Some of them are focused onthe presence or absence of indicator species.Others are based on the different ecologicalstrategies followed by organisms, on the value ofdiversity (by means of indices that measure thespecies richness, models of species abundance,and indices based on the proportional abundanceof species that aim to combine richness anduniformity in a simple expression) or on the energyvariation in the system through changes in thebiomass of individuals.In theory, all indices described in the literaturethat consider those two parameters (speciesFigure 51. Benthic invertebrate fauna quality elements for transitional and coastal waters.Transitional and coastal watersBiological elements • Composition, abundance of benthic • Composition, abundance ofinvertebrate fauna (3 months)benthic invertebrate fauna(3 months)Supporting Morphological conditions: Tidal regime:hydromorphological • Depth variation (6 years) • Freshwater flowelements • Structure and substrate of the • Direction of dominant currentscoastal bed• Wave exposure• Structure of the intertidal zoneSupporting chemical General: Specific pollutants:and physico-chemical • Transparency • Pollution by all priorityelements • Thermal conditions (3 months) substances identified as being• Oxygenation conditions (3 months) discharged into the body of• Salinity (3 months)water (1 month)• Nutrient conditions (3 months) • Pollution by other substancesidentified as being dischargedin significant quantities into thebody of water (3 months)Note: Elements which are only applicable to transitional waters are shown in blue, elements applicable only to coastal waters are shown in red.Where applicable, the sampling frequency indicated in the WFD Annex V is shown in brackets.71


Benthic Reference Conditionscomposition and abundance) could be useful indetecting the environmental situation of asystem. However, many were designed for thecharacteristics of a specific system (whichinvalidates them as widely applicable detectiontools) and others have been rejected due to theirdependence on parameters such as depth orsediment composition, and their unpredictablebehaviour with regard to pollution. Likewise, theuse of purely graphical methods is unacceptable,because they are highly subjective.The guidance developed by the CIS 2.4 (COAST)group provides a list of tools currently available inMember States to classify benthic invertebratefauna.• Norway has a classification tool that includesboth chemical and biotic aspects, using faunaldiversity (Shannon-Wiener and Hulbert indices)and the total organic carbon in the sediment.• Greece has developed a biotic index (BENTIX)applicable in coastal areas, and Spain hasdeveloped another biotic index (AMBI) applicablein European transitional and coastal waters.• The OSPAR Comprehensive Procedureincludes benthic invertebrates as a possibleindicator of indirect eutrophication effectsthrough mortality by oxygen depletion and/orlong term changes in zoobenthos biomassand species composition due to nutrientenrichment.Suitable indices for defining benthicreference conditionsThe use of a single approach does not seemappropriate due to the complexity inherent inassessing the environmental quality of a system.Rather, this should be evaluated by combining asuite of indices which provide complementaryinformation.Additionally, even though the WFD does not takethe biomass parameter into account, in enrichedsituations this is considered to be an importantmetric for the effects of extra energy inputs into asystem.Following those principles, a combination of theShannon-Wiener index, Margalef index, the AMBIMarine Biotic Index and the ABC curves methodby means of the W-statistic is a good option forevaluating the conditions of a particular area. Allthese indices have been applied to widegeographical areas and to zones disturbed bydifferent types of pollution, and they also take intoaccount the different aspects which integrate thebenthic community.• Shannon-Wiener index• Margalef index• AMBI Marine Biotic Index• ABC curves method by means of the W-statisticAll of them have been applied to widegeographical areas and to zones disturbed bydifferent types of pollution.72


Benthic Reference ConditionsThe Shannon-Wiener and Margalef indices providecomplementary diversity measures, as the formertakes proportional abundance of species intoaccount, whilst the latter is focused on speciesenrichment. Furthermore, the use of ABC curvescompares the distribution in number of individualsof the different species of macrobenthiccommunities with the distribution of biomass.Through AMBI, which is based on the presence ofindicator species of polluted and unpolluted zones,the other aspect defined by the WFD has beenconsidered. In this the importance of biologicalindicators is highlighted, in order to establish theecological quality of transitional and coastal waters.Although this index was based on the paradigm ofPearson and Rosenberg, which emphasises theinfluence of organic matter enrichment on benthiccommunities, it was shown to be useful for theassessment of other anthropogenic impacts, suchas physical alterations in the habitat or heavy metalinputs. It has been successfully applied in theAtlantic (North Sea; Bay of Biscay; Southern Spain)and Mediterranean (Spain and Greece) Europeancoastal waters.METHODSApplication of indices as a function ofdata requirements and availabilityDue to an uneven dataset, not all indices could betested for all TICOR systemsFor those where appropriate numeric densitydata were available, the Shannon-Wiener,Margalef and AMBI indices were applied. TheABC curves method was additionally applied insystems where numeric density and biomassdata were available. However, as a combinationof three indices is considered recommendable toevaluate a system, in this case the ABC, AMBIand Margalef indices were applied, as theinformation provided by the Shannon-Wienerindex is already given by the ABC curves method.In a large number of systems only qualitativemetadata were available, so no indices could be73


Benthic Reference ConditionsFigure 52. Application of indices to different systems (including all TICOR systems).Category Type Descriptor Systems Type of data IndicesTransitional A1 Mesotidal stratified estuary Minho No available datasurfaceLimawatersDouroLeçaA2 Mesotidal well-mixed estuary, Ria de Numeric density Shannonhighly variable discharge Aveiro Data for crustaceans MargalefMondego Numeric density Margalefdata, biomass Data ABC methodAMBITagus List of speciesSado No available dataMira Numeric density data MargalefABC methodAMBIArade No available dataGuadiana No available dataCoastal A3 Mesotidal semi-enclosed Albufeira No available datasurface lagoon MelideswatersSto AndréA4 Mesotidal shallow ria Ria Numeric density data ShannonFormosaMargalefAMBIRia de No available dataAlvorA5 Mesotidal exposed Atlantic From No available datacoastMinhountil CaboCarvoeiroA6 Mesotidal moderately From No available dataexposed Atlantic coast CaboCarvoeirountil Pontada PiedadeA7 Mesotidal sheltered coast From No available dataPonta daPiedadeuntil V. R.Sto António74


Benthic Reference ConditionsFigure 53. Summary of indices.SHANNON-WIENER MARGALEF ABC METHOD AMBIH’ = -∑ pi log2pi D = (S-1)/logeN W = ∑ (Bi-Ai)/50(S-1) BI={(0)(%GI)+(1,5)Where n is the number Where S is the number Where Bi is the biomass (%GII)+(3)(%GIII)+of species, and pi is the of species found and N of species i, Ai the (4,5)(%GIV)+(6)proportion of abundance is the total number of abundance of specie (%GV)}/100of species i in a community individuals species i, and S is the GI: Ecological group Iwere species proportions number of species. GII: Ecological group IIare p1, p2, p3... pn.GIII: Ecological group IIIGIV: Ecological group IVGV: Ecological group Vapplied, and only a qualitative assessment wascarried out. Figure 52 shows the indices appliedin each case.The description of the indices is detailed in Figure53. The definition of different ecological levels inthe system according to the values of each indexis shown in Figure 54.Pearson’s correlations were applied to analysethe response of each index as a function ofdifferent environmental variables, and to identifyany significant parallels between the variationpatterns of different indices.RESULTSThe application of the different indices in thevarious systems showed that there is not a typespecificresponse.The results of all the indices were similar, showinga significant correlation (P


Benthic Reference ConditionsWiener indices. This was expected, since bothare diversity indices that provide complementaryinformation.However, none of the cases showed a significantcorrelation between the values of the indicesand the various environmental parameters inthe areas where this analysis was possible. TheAMBI index, on the other hand, has only beensignificantly correlated with such indices when itwas applied to subtidal communities in theMondego estuary (Figure 55). In this system it hasalso been shown that this index does not varywith time, i.e. it is not influenced by changes inabundance. This is important because during thestudy period (1993-1994) there were no changesin environmental stressors.Figure 55. Pearson correlations between the values of the different indices considering thesampling stations located in the two arms of the Mondego estuary.AMBI Shannon-Wiener MargalefShannon-Wiener -0.73**Margalef -0.69* +0.83**W Statistics -0.45* +0.75** +0.72*(*) = P ≤ 0.05; (**) = P ≤ 0.01.The results for the W statistic show that it iscapable of distinguishing between non-disturbed,slightly disturbed and disturbed situations,although in some cases results were confusingdue to the strong dominance of species that arenot pollution indicators (e.g. the mudsnailHydrobia ulvae and the cockle Cerastodermaedule). A similar situation has been observed inprevious studies.As regards specific composition, there is acommon denominator among the systems oftype A2. The dominant species are classified asbelonging to Ecological Group III. These speciesare tolerant to pollution; they may occur undernormal conditions, but their populations arestimulated by organic enrichment. Consequently,low diversity values in many of the systemstaken into account in this study are due tothe dominance of certain species such asLeptocheirus pilosus, Corophium multisetosum,Cyathura carinata, Nereis diversicolor, Carcinusmaenas, Cyathura carinata, Hydrobia ulvae,Scrobicularia plana, and Melinna palmata.In type A4 (Ria Formosa) species belonging toEcological group II (species indifferent toenrichment, always in low densities with nonsignificantvariations with time) mainly dominate,showing, in principle, a better system status.As expected, this dominance leads to low valuesfor the Shannon-Wiener index and in somecases, to a drop in species richness (measuredin this case through the Margalef index).However, it is not necessarily affected by thedominance of certain species. Under certaincircumstances, a higher resource exploitationor natural environmental variation may promotethe development of these species and excludeothers.This study has shown satisfactory results alongthose lines, and it is therefore suggested that thedefinition of ecological status classes may beachieved by combining these indices, as shownin Figure 56.For these reasons, the complementary use ofdifferent indices or methods based on different76


Benthic Reference ConditionsFigure 56. Application of indices as a function of data requirements and data availability.DATA AVAILABILITYQualitative dataQuantitative dataMetadataRough dataNumeric density dataNumeric density and biomass dataShannon-WienerMargalefShannon-WienerMargalefAMBIIdentification ofindividuals down tospecies levelIdentification ofindividuals down tofamily levelABCShannon-WienerMargalefMargalefAMBIABCecological principles is highly recommended indetermining the environmental quality of a system.For those systems where adequate numericdensity data exist, the Shannon-Wiener, Margalefand AMBI indices may be applied. For those withnumeric density and biomass data it isadditionally possible to apply the ABC curvesmethod. However, as the combination of thethree indices is recommended for systemevaluation, in this case the ABC, AMBI andMargalef indices (if species level data exist)should be applied. As an alternative, if only familylevel data exist, the ABC curves method,Shannon-Wiener and Margalef indices should beused.The combination of two or three of the indices(depending on the type of data available) providesa joint evaluation as shown in Figure 57.CONCLUSIONSExperience demonstrates that none of the availablemeasures on biological effects of pollution may beconsidered ideal. The dominance of certain speciesproduces low diversity estimates, although thosespecies belong to ecological groups usually relatedto non-polluted environments. W statistics iscapable of distinguishing between non-disturbed,77


Benthic Reference ConditionsFigure 57. Classification of benthic reference conditions.COMBINATION OF TWO OR THREE OF THE SELECTED INDICESDepending on the type of data availableSTATUSHighHighHighHighHighHighHighHighGoodHigh/GoodHighGoodGoodGoodGoodHighGoodGoodGoodGoodGoodGoodGoodModerateGood/ModerateGoodModerateModerateModerateModerateGoodModerateModerateModerateModerateModerateModerateModeratePoorModerate/PoorModeratePoorPoorPoorPoorModeratePoorPoorPoorPoorPoorBadPoorPoorPoor/BadBadBadPoorBadBadBadBadand disturbed situations but nevertheless, the notso rare dominance of certain species small in sizeand characteristic of non-polluted environmentswill lead to erroneous evaluations. Finally, theclassification of species as indicators of differentgrades of pollution, which constitutes the base ofthe AMBI, often contains subjective elements.Nevertheless, we consider that the combinationof these indices makes up for the defects ofeach one, and result in a good toolset fordetermining ecological quality status, due tothe complementary nature of the ecologicalprinciples of each.Moreover, the AMBI index and the W-statisticcan be considered universal in terms of theirapplicability, i.e. the interpretation of measurementsis independent from the geographic area orthe type of system. Conversely, diversitymeasures and their interpretation are stronglydependent on geographic variation and onthe type of system, in the sense that a givenvalue estimated using a given diversity indexdoes not have the same significance if onecompares warm temperate and boreal systems,or an open coastal area with an estuary locatedat the same latitude.78


Benthic Reference ConditionsTherefore, although in this work guideline valueshave been developed to establish ecologicalstatus, taking into account results from studiesproceeding from various areas, these guidelinesshould be used with caution.KEY REFERENCESBorja, A., Franco, J. & Pérez, V., 2000. A MarineBiotic Index to Establish the Ecological Quality ofSoft-Bottom Benthos Within European Estuarineand Coastal Environments. Mar. Pollut. Bull, 40(12): 1100 - 1114.Borja, A., Muxika, I., & Franco, J., 2003. Theapplication of a Marine Biotic Index to differentimpact sources affecting soft-bottom benthiccommunities along European coasts. Mar. Pollut.Bull., 46 (7): 835-845.Clarke, K.R., 1990. Comparison of dominancecurves. J. Exp. Mar. Biol. Ecol., 138 (1-2): 130-143.Molvær, J., Knutzen, J., Magnusson, J., Rygg, B.,Skei, J & Sørensen., 1997. Classification ofenvironmental quality in fjords and coastalwaters. SFT guidelines. 97:03, 36pp.Paul, J.F., 2003. Developing and applying an indexof environmental integrity for the US Mid-Atlanticregion, J. Env. Management, 67, 175–185.Valiela, I., J. McClelland, J. Hauxwell, P. J. Behr,D. Hersh, & K. Foreman. 1998. Macroalgal bloomsin shallow estuaries: controls and ecophysiologicaland ecosystem consequences. Limnol. Oceanogr.42: 1108-1115.Warwick, R.M., 1986. A new method for detectingeffects on marine macrobenthic communities.Mar. Biol.92:557-562.79


Special IssuesHEAVILY MODIFIED WATER BODIESIntroduction and problem definitionSome water bodies may not achieve “goodecological and chemical status” by 2015 fordifferent reasons. Under certain conditions theWFD permits Member States to identify anddesignate heavily modified water bodies (HMWB)according to WFD Article 4(3).Less stringent objectives will be assigned tothese water bodies: instead of “good ecologicalstatus” (GES), the environmental objective forHMWB is “good ecological potential“ (GEP),which has to be achieved by 2015.The concept of HMWB recognises that manywater bodies have been subject to major physicalalterations so as to allow for a range of wateruses. Article 4(3) (a) lists types of activities whichwere considered likely to result in a water bodybeing designated as a HMWB, from which themost relevant for transitional and coastal watersare:Art. 2, n.º 9 of the WFD defines Heavily ModifiedWater Body as: “a body of surface water whichas a result of physical alterations by humanactivity is substantially changed in character”.the long-term without compromising thecontinuation of the specified use. The conceptof HMWB was created to guarantee themaintenance or improvement of water quality,whilst allowing for the continuation of these uses,which provide valuable social and economicbenefits.The changes to be considered must be significantand substantial and must also be permanent, i.e.those that are limited in time or intermittent arenot considered for the purpose of the definition ofHMWB.These alterations must also result in an obviouschange in character of the water body as, intransitional waters when extensive morphological• Navigation, including port facilities, or recreation;• Flood protection and land drainage.These uses tend to require considerable physicalinterventions which cause hydromorphologicalchanges to water bodies of such a scale thatrestoration to GES may not be achievable even inTo qualify as a HMWB, the water body must be:• Physically altered by human activity;• Substantially changed in character;• Designated under Annex II (Art. 4(3)).81


Special Issuesbe achieved by other means representing abetter environmental option.On the basis of this general guidance, a“substantial” change in hydromorphology will be:• extensive/widespread or profound, or• very obvious in the sense of a major deviationfrom the hydromorphological characteristicspresent before the alterations.Water bodies which have been substantiallychanged only in the morphology shall beconsidered as substantially changed in characterwhen these changes are long term and affecthydrology. A substantial change in hydrologyshall be considered as such when it is caused bya permanent structure, e.g. a dam, and the waterbody will be considered as substantially changedin character even if there are no significantmorphological changes.interventions (dredging and bank artificialization)are performed to create navigation and harbourconditions.A key question for the identification of HMWB isthe definition of substantially changed incharacter”.The WFD presents some general criteria [Art.4, (3)]for this identification as follows:• The changes to hydromorphologicalcharacteristics needed for achieving GESwould have adverse effects on:- The wider environment- Navigation, port facilities, recreation- Water supply, power generation- Regulation flows – flood protection, drainage• The beneficial objectives served by the HMWBcannot (due to cost, technical feasibility, etc.)The environmental objectives for HMWB are GEPand good chemical status, less stringent thanGES because it makes allowances for theecological impacts resulting from those physicalalterations. These objectives are also set inrelation to reference conditions that may bedefined in this context as the “maximumecological potential” (MEP). This is a state wherethe biological status reflects, insofar as possible,that of the closest comparable surface waterbody, but taking into account the HMWBmodifications. GEP accommodates “slightchanges” in biological status from MEP.MethodologyIn the terms of the above concepts, theidentification of sort out an HMWB is carried outafter recognition that GES is not achievable dueto physical transformations, taking into accountthe feasibility of the actions to restore the waterbody in order to achieve GES, and their effect onthe wider environment. A full justification of thedesignation of a water body as HMWB has to beprovided by Member States.82


Special IssuesA flow chart with the methodology foridentification of heavily modified water bodies isshown in Figure 58.Step 4 is part of the characterisation of surfacewaters, which involves the identification anddescription of:• Main “specified uses” of the water body;• Significant anthropogenic pressures [Annex IINo. 1.4]; and• Significant impacts of these pressures onhydromorphology [Annex II No. 1.5].In Step 5, an assessment is made of the risk offailing GES due to hydromorphological changes,rather than other pressures such as toxicsubstances or other quality problems. This distinctionfrom effects resulting from other impacts (e.g. toxiceffects on macro-invertebrates, eutrophicationsymptoms in macrophytes) should be differentiatedas far as possible using e.g. the following criteria,appropriate for transitional and coastal waters:• disruption in river continuity assessment usinglong distance migrating fish species• changes in flow downstream of reservoirs usingmacrophytes• impacts of linear physical alterations such ascoastal defence works using benthic invertebratesand macroalgaeA water body will be provisionally identified asHMWB (step 6) if it complies with the followingcriteria:1. The failure to achieve good status results fromphysical alterations to the hydromorphologicalcharacteristics of a water body. It must not bedue to other impacts such as physicochemicalimpacts (pollution).Figure 58. Methodology for provisional identification of heavily modified water bodies.Water body identification [Art 2(10)] (iterative process).Is the water body artificial? [Art 2(8)]NOYESProcess of designationof ABWNO“Screening”: Are there any changes in hydromorphology?YESDescription of significant changes in hydromorphology.[Annex II No. 1(4)]NOIs it likely that water body will fail good ecological status due tochanges in hydromorphology? [Annex II No. 1(5)]YESIs the water body substantially changed in character due tophysical alterations by human activity? [Art 2(9)]NORelevant enviromental objective:GES [Art 4(1)] or less stringent [Art 4(5)].YESIdentify provisionally as HMWB[Art 5(1) and Annex II No. 1(1)(i)]83


Special Issues2. The water body must be substantially changedin character. This is the case when thereis a major change in the appearance of thewater body. It is a partly subjective decisionas to whether a water body is (a) onlysignificantly changed in character or (b)substantially changed in character, whenprovisional identification as an HMWB may beappropriate.The body of water is substantially changed incharacter when:• It is obvious that the water body is substantiallychanged from its natural condition in apermanent, extensive and profound way.• The change is consistent with the scale ofchange that results from the activities listed inArticle 4(3)(a):• The substantial change in character is the resultof the specified uses which represent equallyimportant sustainable human developmentactivities (either singly or in combination)the complete removal of the physical alteration.The second component requires an assessmentof whether these restoration measures will havesignificant adverse effects on the specified usessuch as losses of important goods and services(e.g. flood protection recreation or navigation),taking into consideration economic and socialeffects. The last component analyses thepossibility of the occurrence of significantadverse effects of restoration measures on thewider environment, i.e. it tests whether therestoration measures required to achieve GES donot create environmental problems elsewhere.The designation test in Article 4(3) (b) considerswhether the beneficial objectives served by themodified characteristics of the water body canreasonably be achieved by other means which are:• technically feasible• a significantly better environmental option• not disproportionately costly.The final designation as HMWB of theprovisionally identified water bodies implies thecompletion of the designation procedure asspecified under Article 4(3) (a) & (b). These testsare designed to ensure that HMWB are onlydesignated where there are no reasonableopportunities for achieving good status within awater body, and are therefore water bodyspecific. The methodology and decision rules forfinal designation are presented in Figure 59.The designation test in Article 4(3) (a) has threecomponents, dealing with “restoration measures”for achieving GES, with their “adverse effects” onthe specific uses and on the wider environment.The hydromorphological changes for achievingGES, i.e. the restoration measures to beanalysed, may range from measures aimed atreducing the environmental impact of thephysical alteration (e.g. increased compensationflows or fish passages) to measures resulting in84


Special IssuesFigure 59. Final designation of heavily modified water bodies.Provisionally identified HMWBIdentification of restoration measures to achieve GESDesignation tests 4(3) (b) Designation tests 4(3) (a)NONOYESNOYESIs the physical alteration connected to a current specified use?Would the restoration measures have significant adverse effectson the specified uses?Would the restoration measures have significant adverse effectson the wider enviroment?YESYESNOAre there other means of providing the beneficial objectivesserved by the physical alteration?YESAre these other means tecnically feasible?YESAre these other means a better environmental option?YESAre these other means disproportional costly?NOWill these other means allow the achievement of GES?NOYESNONOIs the failure to achieve GES caused by physical alterations?YESDesignate as HMWBNO“Natural water bodies”Water bodies for which other means that fulfilthese three criteria can be found, and canachieve the beneficial objectives of the modifiedcharacteristics of the water body may not bedesignated as HMWB. The existing specified usemay, in some cases, be abandoned and thephysical alterations removed so that good statuscan be achieved.A water body may be designated as HMWB if ithas completed the designation procedureinvolving, if applicable, both designation tests(Figure 59).If there are no significant adverse effects either onthe specified uses or on the wider environment,or there are “other means” of delivering the85


Special Issuesbeneficial objectives then the water body shouldbe regarded as natural.ResultsA preliminary exercise was carried out in order toidentify possible candidates to the classificationas HMWB within Portuguese transitional andcoastal waters. The process should start with theassessment of whether some of the water bodiesconsidered in TICOR are likely not to comply withthe GES objectives. This is clearly not feasible atthis stage, nor was it an objective of the TICORproject. Nevertheless, it was deemed useful toperform the exercise starting from theidentification of the TICOR systems that, byexpert judgement, were considered significantlymodified on the basis of their physicalcharacteristics. The Douro, Sado and Guadianatransitional waters were selected due to differentreasons. The interventions, the uses associatedwith them and their effects on the hydrology,morphology and on ecological characteristics aresummarised in Figure 60.The tentative application of the designation testsis not fully feasible at this stage as the possible“distance” to GES is not identifiable. It istherefore also not possible to identify “restorationmeasures” to achieve GES.Nevertheless, it appears that the physicalalterations are connected with uses listed in theWFD and that most of the foreseeable measures/physical interventions may have “significantadverse effects” on those uses.The decision rule shown in Figure 59 will thenimply the test (step 8.1) of whether there are otherFigure 60. Physical interventions and effects on candidate HMWB systems.ChangesPhysical interventions Associated uses Hydrology Morphology EcologyDouro Crestuma dam Energy production River flow Artificial weir PhysicalCatchment intervention Domestic water modification limit of the barriersupply estuary to fishmigrationSado Catchment intervention Domestic and River flow Possible Habitat(regularisation index > 1) agricultural water modification change in changeArtificial banks, supply current in (reductiondredging and land Energy production patterns of intertidalreclamation Port activity Possible areas andIndustrial settlement effects on wetlands)Conversion of salt sediment Possiblepans for aquaculture dynamics changeon watertransparencyGuadiana Catchment intervention Domestic and River flow Possible Physical(regularisation index > 1) agricultural water modification effects on barrierAlqueva – Pedrógão supply sediment to fishand Andévalo-Chanza Energy production dynamics migrationsystems86


Special Issuesmeans of providing the beneficial objectivesserved by the physical alteration. The decision isboth system and use dependent, although thefollowing situations may be identified: (a) energymay be obtained from alternative sources; (b)water supply in the present climatic region will notbe available by alternative means; (c) portfacilities are dependent on natural conditions andmay also have no alternatives.The feasibility of the other means and, in particular,their declaration as a “better” environmental optionwould probably lead directly to the designation ofall above listed systems as HMWB.PRESSURES AND IMPACTSThe analysis of the pressures component of TICORfollows the “Guidance for the analysis of pressuresand impacts in accordance with the WFD”. Fourgroups of pressures, related impacts and datasources most relevant for Portuguese transitionaland coastal waters have been reviewed.quality degradation, with adverse effects onuses such as bathing water quality andfisheries. Further study is required on adverseeffects on the biota and ecosystems;• Toxic pollution. This results from a number ofsources, including industry, urban areas, infrastructure,agriculture and navigation. Resultingimpacts are often poorly understood for lack ofdetailed studies and data;• Nutrients. These are associated mostly withagricultural run-off, although other sources mayalso be relevant (air pollution, urban sewageand run-off). The major impact associated withnutrients is eutrophication. This is a potentialissue in more enclosed transitional and coastalwaters, less so in open coastal waters.Key approaches• Polluting emissions• Water regime• Morphology• BiologyPolluting emissionsTransitional and coastal waters in Portugal aresubjected mostly from the following kinds ofpollution:• Organic biodegradable pollution, alsoassociated with microbiological contamination,This results from untreated or undertreatedurban and industrial sewage, and agriculturalrunoff. Resulting impacts, common intransitional waters and occasionally in coastalwaters, include chemical and biological water87


Special IssuesIt should be noted here that impacts resultingfrom a complex set of pressures (e.g. differentand varying pollution sources) are best studied inliving species that are most sensitive and/ornatural integrators, such as top predators orbenthic fauna.Quantification of pollution pressures shouldinclude a broad range of inputs into all transitionaland coastal waters.All polluting loads should be located with the aidof GIS, and accounted for at least on a yearlybasis, to allow for a general trend analysis ofpolluting pressure. More detailed temporaldiscrimination should be used whenevernecessary to model pressure-impact interactions.Some impacts are readily visible, even if they arenot the most worrisome - e.g. the internationalproject CoastWatch, managed in Portugal by anenvironmental NGO, regularly produces informationon the amount and type of garbage that appearsQuantification of inputs• Rivers. Major rivers tributary to transitional or coastal water should be identified. Information ofpollution load in these should be available from river water management, or must be collected. Smalltributaries may be treated as non-point sources, if adequate modelling is available• Industrial IPPC point sources. These should be fully inventoried and quantified according to EuropeanPollution Emission Register (EPER) guidelines; OSPAR harmonised quantification and reportprocedures (HARP) should be added as appropriate• Industrial non-IPPC point sources. The EPER guidelines should be used as possible. Industry withdischarge permits should be fully inventoried. When relevant pollution information is not available for asource, the maximum allowed load derived from the emission permit should be used instead. Variablesnot included in the permit may be disregarded• Urban point sources. Urban discharges, from both treatment plants and untreated sewage systemsshould be fully inventoried. Pollution quantification should be made for all discharges, based on actualmeasurements, permit limits (if the treatment is working apparently properly but there are no data), orcomputed from estimated loads of population and small industry• Agricultural run-off. Research is required, because it is certain that it is relevant but existing scientificknowledge is not enough to quantify pressures, or to relate land use directly to such pressures. Landuse information is more or less available, but that is not enough per se. Studies from other countriesare not readily applied in Portugal due to major differences in soil, climate and agricultural practice• Urban and infra-structure run-off. Research is also needed. Existing land use information is adequate,but it is not enough to quantify pollution pressure. Existing studies are scarce and unrepresentative, butthey do indicate that the issue is relevant• Navigation. Water pollution related to navigation is of high importance for Portugal, especially in thecoastal waters, where the major navigation lane between Gibraltar and Northern Europe is located.About one hundred ships per day cross those waters, about half of those oil tankers. Several seriousoil spills have highlighted in the worst possible way how vulnerable the Iberian coast is to maritimepollution hazards. However, a large part of maritime pollution is actually due to "operational", deliberatedischarge of hydrocarbon-contaminated effluents88


Special Issueson the shoreline. Navigation-related pressuresand impacts could best be monitored byimplementing an integrated information systemsuch as the InfoZEE model.Water regimeWater regime comprehends a range of issues,from hard changes in the flow in the transitionaland coastal waters, to freshwater inflow.Changes in freshwater or sediment inflow, eitherby water abduction, sand extraction or flowregularisation with dams in the tributarywatersheds, may profoundly change large tractsof the transitional ecosystem. This is particularlyrelevant in southern Portugal, because the rivershave a markedly torrential regime, and mostwetlands that used to act as flow buffers nolonger exist. Changes in freshwater flow andsediment flow (mostly sand) may also influencethe coastal ecosystem if fish nurseries areaffected.Hard changes in the estuaries (e.g. estuary mouthdamming) do not exist in Portugal. Nevertheless,flow in some transitional and closed coastalwaters is heavily influenced by bar protection andharbour works. Coastal lagoons seasonally opento the ocean are often opened artificially toimprove their water quality.Water flow in open coastal waters in thePortuguese coast is not influenced by humanPressure indices• Water abduction index = (upstream abduction) / (actual flow + upstream abduction) = 1 – (actual flow /natural flow)• Regularisation index = (reservoir volume in the waterbasin) / (average annual freshwater discharge)• Sediment abduction index = 1 – (actual sediment flow / natural sediment flow)action, although it does influence water quality,coastal erosion, and fisheries.The importance of freshwater and sediment flowchange in transitional and closed coastal waterscan be fairly easily perceived with three simplepressure indices.The effects of bar and waterworks are moredifficult to quantify, because they depend on verycomplex interactions between river water flow,solid flow and coastal dynamics.Evaluation of impacts has to be performed on acase by case basis. As a guidance, the higher thePressure indices• Shoreline artificialisation index = (artificialisedshore length) / (total shore length)value of these indices, the more likely there will besignificant impacts from water regime change,meriting a correspondingly more thorough impactanalysis. In the case of transitional waters, thesediment abduction index may be computed forupstream and downstream sections.MorphologyCommon direct pressures regarding themorphology of coastal and transitional watersinclude:• Harbour and bar protection works;• Shoreline artificialisation;• Coastal protection heavy works;• Navigation channel dredging;• Sand extraction, either in the catchment area orin the water body itself;89


Special Issuesrelated to coastal erosion. This may or may nothave a significant impact depending on sitesensitivity and size of the intervention ascompared to total water body size. Actual impactis very site-specific and must be reviewed on acase by case basis.BiologyEcosystem quality is influenced by a number offactors, including the above mentioned pollution,water flow changes and morphology changes.Moreover, it can be directly affected by otherhuman activities, namely:• Landfilling to create urban, infra-structure oragricultural area.All pressures consisting in heavy works are readilyidentifiable on aerial or satellite photography.Additional information may be gathered from otherparties, such as local authorities or environmentalNGOs. Port authorities have adequate data onnavigation channel dredging. Sand extraction isthe worst covered sector, due to lack of adequatecontrol, but can be swiftly remedied.Shoreline artificialisation is correlated to anumber of impacts, including coastal erosion andpollution from different human activities.A simple index for evaluating the importance ofthese pressures is shown opposite.The higher the value of the index, the higher theprobability of impacts resulting from suchpressures.Other pressures such as dredging, sandextraction or landfilling have the immediate effectof destroying local ecosystems, and may also be• Fisheries. Although seldom associated with theconcept of “water quality”, fisheries are amongthe most important pressures imposed ontransitional and coastal waters. Actual impactdepends on a number of factors, but it isclosely related to the degree of exploitation offisheries stocks. There is much information onthe impact of fisheries, but there is as yet noadequate management model. Portuguesefisheries (like European fisheries in general) arelacking both better research and bettermanagement policies.• Aquaculture. This is an expanding activity, thatmay have a significant impact on the waterbody, mainly due to direct destruction of localecosystems, introduction of alien species, andpollution related to fish-farming techniques.More research is needed for proper assessmentof such impacts.ReportingFor purposes of reporting, it is useful thatinformation is presented using synthetic indicatorsthat can be readily perceived by the public.Environmental impacts are very difficult toaggregate. It is simpler to select a few keyindicators that are representative of whateverissue is being communicated.Environmental pressures, on the other hand, areeasier to standardise and it is useful that they90


Special Issuesshould be presented in an aggregate form withmethods such as the “Ecological Footprint” or“EcoBlock”.KEY REFERENCESEC, DG Environment, 2002. Guidance for theanalysis of pressures and impacts in accordancewith the WFD.EC, DG Environment, 2002. Guidance documentfor EPER implementation,http://europa.eu.int/comm/environment/ippc/eper/CIS Working Group 2.2, 2003. Guidance documenton the identification and designation of heavilymodified and artificial water bodies. (Versionagreed at the meeting of the Water Directors on21/22 November 2002 in Copenhagen.GEOTA. CoastWatch Portugal.http://www.despodata.pt/geota/coastwatchKampa, E. and Hansen, W., 2003. Draft SynthesisReport on the Identification and Designation ofHeavily Modified Water Bodies. CIS WorkingGroup 2.2 on Heavily Modified Water Bodies.Ecologic, Institute for International and EuropeanEnvironmental Policy, Berlin, Brussels.Joanaz de Melo, J., Andrade, F., Afonso, J.R.,Leitão, P., Piedade, J. & Santana, P., 2002. InfoZEE- Information System for Management andSurveillance of the Exclusive Economic Zone. In:Proceedings of International workshop “Goodpractices on coastal zone management andcoastal defence”. FEUP/EUCC, Porto, Portugal, 7-8 June 2002. http://gasa.dcea.fct.unl.pt/infozee/Joanaz de Melo, J. & Pegado, C., 2002. EcoBlock –A method for integrated environmental performanceevaluation of companies and products. In:Proceedings of the Fifth International Conference onEcoBalance, 399-402. The Society of NontraditionalTechnology, Tsukuba, Japan. November2002. http://gasa.dcea.fct.unl.pt/ecoblock/91


General ConclusionsPortugal has a number of important estuaries,which fall under the category of transitionalwaters – two of these, and parts of the riverswhich flow into them, form the northwestern andsoutheastern borders with Spain. Portugal has anextensive coastal area, which delimits the countryto the west and to the south.The Typology and Reference Conditions (TICOR)study aimed to provide a framework for appropriatecoastal management in Portugal, following therequirements of the Water Framework Directive.The team carrying out this work reviewed a broadrange of issues, ranging from classification ofdifferent systems, division into system types, andexamination of approaches to ecological qualitystatus and the definition of reference conditions fortransitional and coastal waters.In order to address some of these issues, theTICOR project was carried out.The key outputs of TICOR are presented in thisbook, which begins with a brief introduction toTICOR objectives• Develop an integrated approach for all Portuguese coastal and transitional waters for the application ofthe Water Framework Directive (WFD)• Provide the data framework and methodology for delimiting and typing Portuguese coastal andtransitional systems• Assemble the data required for WFD typology and first generation (G1) reference conditions, based on WFDcriteria and on the guidance provided by the Common Implementation Strategy working group COAST• Deliver a set of maps for typology of a key subset of Portuguese coastal and transitional waters• Derive a set of G1 reference conditions for Portuguese coastal and transitional types• Review the special issues of Heavily Modified Water Bodies and of Pressures and their application toPortuguese coastal and transitional watersthe WFD, and to the main aspects concerningtransitional and coastal waters, and follows with afurther seven chapters. Every effort has been madeto allow each chapter to be readable on its own,93


General Conclusionsby including the basic components of the theme,from concepts to methods and results. The toolschapter provides an overview of the techniquesused for the different parts of the work.IntroductionWFD and guidance & key objectivesMethodologyDetails on the TICOR processToolsSummary of tools used in TICORSystems, limits & morphologyDefinitions for transitional & coastal waters, GISpresentation of areas and volumesTypologyClassification of transitional & coastal waters intoseven typesPelagic reference conditionsReview of the state of the art for classificationtools, and suggested approaches for defining firstgeneration pelagic reference conditionsBenthic reference conditionsReview of the state of the art for classificationtools, and suggested approaches for defining firstgeneration benthic reference conditionsSpecial issuesHeavily Modified Water Bodies and generalapproach to environmental pressuresA summary of the key outputs and findings ofTICOR are presented below.DataOver 600,000 records of data for Portuguesetransitional and coastal waters have beenarchived in relational databases during theproject. These are available on the internet, andcontain parameters ranging from water andsediment quality to species lists, covering ten94


General ConclusionsFigure 61. Areas and volumes of TICOR systems.System name Classification Area (km 2 ) Volume (10 6 m 3 )Minho estuary Transitional 23 67Lima estuary Transitional 5 19Douro estuary Transitional 5 39Ria de Aveiro Transitional 60 84Mondego estuary Transitional 9 21Tagus estuary Transitional 330 2 200Sado estuary Transitional 170 850Mira estuary Transitional 3 17Guadiana estuary Transitional 18 96Ria Formosa Coastal 49 92Exposed Atlantic coast Coastal 3 200 195 000Moderately exposed Atlantic coast Coastal 4 200 295 900Sheltered Atlantic coast Coastal 1 000 27 600Note: Different colours correspond to different types.transitional and coastal waters, and in somecases spanning over seventy years. These datawere the foundation for the work which has beendeveloped, and are an important referencecollection of historical information on which futuremonitoring and research activities may build.Systems, limits and morphologyTICOR addressed ten transitional and inshorecoastal systems, as well as the coastline ofcontinental Portugal (Figure 61). The project didnot consider the areas of Madeira and Azores.A geographic information system (GIS) wasdeveloped for all the systems, and was used as aframework for the subsequent definition of limits,areas and volumes.From a total of 44 transitional or coastal systemsin Portugal, about half are in class A (≤ 0.3 km 2 ).The other 48% are distributed in other classes.Class D (≥ 1.0 km 2 ) is the most representative ofthese.The systems studied in TICOR, together with theirclassification into transitional or coastal watersand morphological data, are shown in Figure 61.95


General ConclusionsTypologySeven different types of transitional and coastalwaters were defined for Portugal, based on theconsideration that the number of types should berelatively small but should accurately reflect theexisting diversity of systems (Figure 62).Two transitional water types were defined,corresponding to estuarine systems from thenorthern and southern parts of Portugal. Type A2,mesotidal well-mixed estuary with irregular riverdischarge, is envisaged to be almost unique inthe European Union, due to the combination ofhighly variable freshwater discharge and mesotidalregime. Additionally, two semi-enclosed coastaltypes were defined, as well as three open coastaltypes, which were judged to be sufficient todescribe the entire Atlantic coastline. Of thesethree, type A6, mesotidal moderately exposedAtlantic coast, is considered to be unique to theEuropean Union, because it combines coldernorth-east Atlantic and warmer Mediterraneaninfluences with the dynamics of a narrow shelf.The type names and descriptions are shown inFigure 62.The rationale for each type is explained in theTypology chapter, and the areas and volumes forthe different types were determined with basis onthe GIS. Some results are presented also on thedistribution of these morphological data amongtypes, and a discussion of types which maypotentially be common to other EU member statesis made. The most likely candidate types are: A1,A3, A5 and A7.Figure 62. Proposed typology and classification of systems larger that 1 km 2 .Type Descriptor Systems larger than 1 km 2A1 Mesotidal stratified estuary Minho estuaryLima estuaryDouro estuaryLeça estuaryA2 Mesotidal well-mixed estuary Ria de Aveirowith irregular river dischargeMondego estuaryTagus estuarySado estuaryMira estuaryArade estuaryGuadiana estuaryA3 Mesotidal semi-enclosed lagoon Óbidos lagoonAlbufeira lagoonSt. André lagoonA4 Mesotidal shallow lagoon Ria de AlvorRia FormosaA5 Mesotidal exposed Atlantic coast From the Minho estuary until Cabo CarvoeiroA6 Mesotidal moderately exposed From Cabo Carvoeiro until Ponta da PiedadeAtlantic coastA7 Mesotidal sheltered coast From Ponta da Piedade until Vila Real de Sto. AntónioNote: TICOR systems shown in blue.96


General ConclusionsMain findings for pelagic reference coditions• There are sufficient data in most cases for establishing reference conditions for phytoplantonabundance, biomass and composition. Some gaps exist for type A1 and for open coastal waters• The supporting quality element nutrients should be measured in order to monitor elemental ratios, andto support the evaluation of pressures, but no clear link between dissolved nutrients in the watercolumn and phytoplankton biomass and abundance could be established• Phytoplankton composition differs clearly between transitional water types. Some questions are raisedabout the Sado estuary, which behaves like a coastal lagoon for this element• Phytoplankton composition in transitional waters is potentially linked to water residence time. Thisshould be further explored, and if appropriate taken into account when establishing referenceconditions• Phytoplankton abundance may be adequately represented by biomass, using chlorophyll a as a proxy• Phytoplankton biomass and abundance should be assessed using an integrated methodology, becauseorganic enrichment effects may be manifested also in changes to benthic flora. The use of the ASSETSapproach, developed from the U.S. National Estuarine Eutrophication Assessment procedure isrecommended• Ecological status for fish is potentially best evaluated using Indices of Biotic Integrity (IBI)Pelagic reference conditionsA review was carried out of the approaches thatmay be used for determination of ecological qualitystatus in phytoplankton and fish, the latter qualityelement only for transitional waters. The relevanceof the various supporting quality elements wasalso analysed, using relationships developedfrom the TICOR databases and other sources.Benthic reference conditionsA review was carried out of the approaches thatmay be used for determination of ecologicalquality status of benthic quality elements, bothfor aquatic flora and fauna. A potential method forestablishing a scale for reference conditions ofbenthic plants based on relative areal distributionand biomass of opportunistic and long-livedspecies is outlined. The method needs to berefined and tested.The data collected on benthic macrofauna wereused extensively to explore a number of differentindices, across a range of transitional water types.97


General ConclusionsFigure 63. Application of indices as a function of data requirements and data availability.DATA AVAILABILITYQualitative dataQuantitative dataMetadataRough dataNumeric density dataNumeric density and biomass dataShannon-WienerShannon-WienerIdentification ofIdentification ofMargalefMargalefindividuals down toindividuals down toAMBIspecies levelfamily levelABCShannon-WienerMargalefMargalefAMBIABCFigure 63 shows a synthesis of the work carried out.A first generation approach to ecological qualitystatus may be carried out by using a combinationof appropriate indices, based on data availability.Special issuesTwo key areas were examined in the SpecialIssues chapter: Heavily Modified Water Bodiesand Pressure elements.One key finding of this part of the work is that there does not seem to be a basis for type differentiationof reference conditions for benthic fauna in transitional waters, in the application of the AMBI index andW-statistic. However, diversity indices may be regarded as type-specific, and will help to differentiatetypes in future developments of this method.For the first issue, TICOR results are based ondata developed by the relevant guidance group,defining the evaluation process that should befollowed for classification.The pressures guidance document was also usedas a framework for discussion of this issue, thefocus of the TICOR work is on the developmentof localised guidelines for the most relevantpressures on Portuguese transitional and coastalsystems.98


TYPOLOGY AND REFERENCE CONDITIONSFOR PORTUGUESE TRANSITIONAL AND COASTAL WATERSDevelopment of Guidelines for the Applicationof the European Union Water Framework DirectiveEDITOR INAGInstituto da Águawww.inag.ptIMAR - Institute of Marine Researchwww.imar.ptDESIGN AND PRODUCTIONIdeias Virtuaisideiasvirtuais@mail.telepac.ptPHOTOSJoana Dilãojoanadilao@sapo.ptISBN?????????????LEGAL DEPOSIT???????????????N. OF COPIES??????????Mês??????? 2003??????© INAG - instituto da Água • IMAR - Institute of Marine Research


Portugal em AcçãoMINISTÉRIO DAS CIDADES,ORDENAMENTO DOTERRITÓRIO E AMBIENTE

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