A Model for the Evaluation and Management of Contaminants of ...

A Model for the Evaluation and Management of 

Contaminants of Concern in Water, Sediment, and 

Biota in the NY/NJ Harbor Estuary 

INSTRUCTIONS FOR SUBMITTING PROPOSALS 

On behalf of the Contamination Assessment and Reduction Project (CARP) of the NY/NJ Harbor 

Estuary Program (HEP), The Hudson River Foundation (HRF) seeks proposals from contractors to 

develop and apply mathematical modeling tools to integrate available ambient concentration and loading 

data to evaluate contaminant fate, transport and bioaccumulation in the NY/NJ Harbor Estuary. These 

models may also be used to provide predictive capability to dredged material and contaminated sediment 

managers who are evaluating the consequences of various remedial actions. 

A tiered approach will be taken in developing models for the CARP. Tier-one will involve selecting, 

refining and applying existing large-space-scale, seasonal-time-scale model(s) for contaminant fate and 

bioaccumulation. Tier-two will be the development of explicit, finer-scale models that couple 

hydrodynamics, water quality, and cohesive sediment transport. A detailed Request for Proposals for A 

Model for the Evaluation and Management of Contaminants of Concern in Water, Sediment, and 

Biota in the NY/NJ Harbor Estuary is attached. 

I. Background 

The CARP is an estuary-wide program to measure and model the sources and ambient levels of 

contaminants in the New York/New Jersey Harbor Estuary system. Components of the program include 

quantification of sources (sewage treatment plants, combined sewer overflows, tributaries, storm water 

overflows, atmospheric deposition, etc.) of organic and inorganic contaminants and ambient levels of 

those contaminants in water, sediments, and biota. Data collected under this program will be used to 

make management decisions about dredged material disposal in the Harbor region and to provide a 

baseline for future monitoring of these parameters to determine ecosystem health. 

The sampling and analysis programs of the states of New York and New Jersey, defined in the detailed 

work plans Sources and Loadings of Toxic Substances to New York Harbor (New York=s work plan) 

and the New Jersey Toxics Reduction Workplan, comprise the majority of the field and laboratory 

measurements of the CARP. These documents are available from the Hudson River Foundation or by 

downloading from the HRF web site at www.hudsonriver.org/hep/carp.htm. 

Financial resources for model development are being provided to the Hudson River Foundation by the 

Port Authority of New York and New Jersey as part of the Joint Dredging Plan for the Port of New 

York and New Jersey. The requirements and conditions of the agreement between the Port Authority 

and the Foundation are applicable to any contractors when the Foundation selects to perform services in 

connection with that agreement. Such requirements and conditions will be included in contractual 

arrangements between the Foundation and the modeling contractor.

II. Criteria for Evaluating Proposals 

Proposals will be evaluated using the following criteria: 

$ Demonstrated experience in conducting similar work successfully 

$ Qualifications of the personnel to be assigned to the program 

$ Merit of proposed approach to accomplishing objectives outlined in the RFP 

$ Likelihood of success in meeting stated objectives 

$ Cost 

III. Proposal Submittal Information 

Proposals should be no longer than 20 pages and include the following elements: 

$ Cover Page (please use attached form) 

$ Statement of Work: Proposers should present a clear and detailed description of the modeling 

approach they intend to follow. The discussion shall include reasons for acceptance or rejection 

of elements of the modeling approach outlined in the attached RFP. Where modifications are 

offered, justification should be given. Proposers should relate relevant experiences to the project 

they are now proposing. The Statement of Work should generally be no longer than 20 pages. 

$ Qualifications and CV(s) of all project personnel 

$ Statement of related experience of the contractor 

$ Itemized budget: (Please use the forms provided.) The project budget is to be shown in two 

ways: (1) Total project budget by category of expense on the attached Hudson River 

Foundation form, and (2) Total project budget by task. Tasks for this contract are described in 

bulleted lists in sections VII and VIII on pages 11-17 of the attached Request for Proposals. For 

each task, proposals should provide a detailed cost breakdown. 

Project period: Four years 

Approximate level of funding for entire modeling project: $2,500,000.00 

Deadline: 

Proposals (original plus 20 copies) must be received by the office listed below by the 

close of business on Friday, September 8, 2000. 

Contacts: Submit proposals to: Dr. Dennis Suszkowski 

Hudson River Foundation 

40 West 20 th Street,9 th Floor 

New York, NY 10011 

For more information contact Dr. Suszkowski at (212) 924-8290 or dennis@hudsonriver.org.

NY/NJ Harbor Estuary Program 

Contamination Assessment and Reduction Project 

Modeling 

Proposal Cover Page 


Proposal #: 

For HRF use 

Name of Firm/Contractor: 

Summary of Proposal: 

Amount Requested: 

Total: 

$________________ 

Year-1: 

Year-2: 

Year-3: 

Year-4: 

$________________ 

$________________ 

$________________ 

$________________ 

Principal Investigator(s): 

(Name, Title, Address, Phone, Fax, e-mail) 

Contract Administrator: 

(Name, Title, Address, Phone) 

Proposal Approval: 

Payments to be sent to: 

(Name, Title, Address, Phone) 

Applicant's Tax Status 

❑ 

❑ 

❑ 

❑ 

❑ 

Tax Exempt under 501(c)3 

Not a Private Foundation 

under Sec. 509(a) 

Private Foundation 

Not Tax-Exempt 

Government 

_________________________ __________ 

Institutional Representative Signature Date 

(Include typed name & title below if different from Contract Administrator) 

_________________________ 

Principal Investigator Signature 

__________ 

Date

PROPOSAL BUDGET SUMMARY 

Hudson River Foundation/CARP Modeling 

FOR HRF USE 

Grant # 

Principal Investigator 

Proposal # 

Organization 

$ 

REQUESTED 

FROM HRF 

$ 

COST SHARING 

$ 

TOTAL COST 

DIRECT COSTS 

Labor (list personnel by name, support personnel by category) 

1) 

2) 

3) 

4) 

5) 

6) 

A. Total Labor Costs 

B. Fringe Benefits 

Non-Expendable Equipment (list item and amount for each item exceeding $500) 

C. Total Non-Expendable Equipment 

D. Expendable equipment 

E. Equipment Rental 

F. Boat Use 

G. Computer Services 

H. Consultant Services (other than subcontracts) 

I. Travel 

J. Publication Costs 

Office Support (only when directly relevant to performance of the proposed project) 

Materials and Supplies 

Telephone 

Postage 

Copying and Printing 

K. Total Ofice Support 

L. Miscellaneous (specify) 

M. TOTAL DIRECT COSTS (A through L) 

N. INDIRECT COSTS/OVERHEAD (specify) 

O. SUBCONTRACTS (attach separate budgets) 

P. TOTAL COSTS (M + N + O)

Budget Breakdown by Task 

CARP Modeling Proposal 


FOR HRF USE 

Proposal # 

Please note: Please provide detailed descriptions of the budget 

for each task, including amount of time each task will require, 

on an attached sheet(s). 

Principal Investigator 

Organization 

$ 

TOTAL COST 

TASK (see RFP for further details) 

1-1: Select a large-space-scale, seasonal-time-scale model 

1-2: Refine the selected model(s) to ensure inclusion of additonal features 

1-3: Review and compile recent baseline data for the Harbor 

1-4: Compile new/updated loading estimates for contaminants 

1-5: Conduct calibrations/verifications using availalble CARP monitoring data 

1-6: Conduct model sensitivity runs 

1-7: Conduct model scenario analyses 

1-8: Develop user interface for simulating additional scenarios 

1-9: Develop modeling approach for evaluating sediment toxicity 

TOTAL, TASKS 1-1 - 1-9 

2-1: Develop Tier-2 model(s) 

2-2: Review NY and NJ sampling designs and recommend modifications 


3-1: Develop user manuals for applying Tier 1 and Tier 2 models 

3-2: Provide training to CARP participants on the use of models 

3-3: Provide recommendation and cost estimate for long-term model maintenance 


GRAND TOTAL, ALL TASKS

A Model for the Evaluation and 

Management of Contaminants of 

Concern 

in Water, Sediment, and Biota 

in the 

NY/NJ Harbor Estuary 

Request For Proposals 

July 21, 2000 


40 West 20 th Street, 9 th floor 

New York, NY 10011

I. Introduction 

A consortium of state, federal and non-profit agencies is collaborating on a project to 

establish a scientifically sound basis for mitigating chemical contamination in the New 

York/New Jersey Harbor Estuary. This project – the Contamination Assessment and 

Reduction Project (CARP) – is an outgrowth of the former Sediment Contaminant 

Reduction Work Group (SCRWG) of the New York/New Jersey Harbor Estuary Program 

(HEP). The principal tasks to be undertaken by CARP are those that have been 

recommended in the final Comprehensive Conservation and Management Plan (CCMP) 

for the HEP. These tasks include investigations of the interactions of contaminants with 

water, sediment and biota, and the response of such interactions to changing contaminant 

inputs throughout the Estuary. 

The contamination of the estuary is resulting in economic hardships (e.g., dredging delays 

and more expensive disposal options), public health concerns (e.g., dredged material 

handling and disposal, and fish consumption advisories), and ecological concerns (e.g., 

contaminant-related acute and chronic effects on aquatic life). 

Recently, CARP began work on a bi-state effort to assess ambient concentrations of 

hydrophobic organic contaminants and heavy metals in the NY/NJ Harbor Estuary, and to 

quantify contaminant loads to the Estuary. The data collection efforts are primarily being 

carried out under the supervision of the New York State Department of Environmental 

Conservation (NYSDEC) and the New Jersey Department of Environmental Protection 

(NJDEP). The CARP will provide the technical basis, through comprehensive data 

collection and modeling, for an estuary-wide contaminant reduction strategy. 

Overall, the CARP serves as a mechanism for articulating the Harbor contamination reduction 

goals contained in the HEP CCMP and supports the following objectives: 

• Development of a long-term Harbor monitoring and management system that tracks 

progress of contamination reduction plans; 

• Reduction of levels of the contaminants of concern such that water quality standards 

are met, dredged sediments meet all requirements for upland beneficial use or for 

remediation at the Historic Area Remediation Site (HARS), and fish/shellfish are 

safe for human consumption; 

• Identification and trackdown of significant sources of the contaminants of concern to 

water, sediment and biota, including existing sediment “hot spots;” 

• Development of management tools to assess, under different management 

scenarios, when appropriate water quality criteria and standards for the parameters 

of concern will be met in the water column; 

• Development of management tools to assess, under different management 

scenarios, the time frame required for Harbor sediments to support a healthy 

benthic community system and meet all state and federal requirements for upland 

beneficial use or use at the HARS. 

• Development of management tools for determining Total Maximum Daily Loads 

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(TMDLs), as required by agreements between the U.S. Environmental Protection 

Agency (EPA) and the states of New York and New Jersey for substances of 

concern, in all water, sediment and/or biota of the NY/NJ Harbor. 

• Development of management tools to predict concentrations of other substances 

determined by the Toxics Workgroup of HEP to be of concern in water, sediment, 

and biota; 

• Development of a management tool to predict effects of changes in Harbor 

bathymetry on the distribution of the contaminants of concern; and 

• Development of a management tool to facilitate potential Natural Resource 

Damage Claims. 

It is the consensus of CARP participants that mathematical modeling tools are needed to 

help the region address some or all of these goals. Such models provide a means for 

integrating available ambient concentration and loading data in a mass balance framework 

so that dominant fate and transport processes can be identified. Moreover, these models 

may provide the predictive capability that managers and scientists need to assess the 

consequences of various remedial actions (e.g., additional source trackdown efforts, 

remediation of contaminated sediments, TMDLs/WLAs/LAs, clean-up of contaminated 

sites) and to predict the time frames required for reductions in contaminant levels in Harbor 

waters, sediments and biota. Accordingly, this RFP provides generalized tasks and 

specifications for the development and application of such models. 

II. 

Modeling Questions 

The specific questions that need to be addressed through modeling are as follows: 

What is the relative importance of specific loadings of contaminants to the quality 

of dredged material today? (What current pollutant sources/ loadings can be linked to 

contamination problems (i.e., criteria violations) at dredging locations in New York Harbor 

and what proportion of the problem is attributed to each source?) 

How will the quality of newly deposited sediments at future dredging sites change if no 

contaminant reduction actions are taken? How will the sediments be affected if specific 

contaminated loadings are reduced or eliminated? 

A. How long will it take for improvement in newly deposited sediment quality after 

contaminant reductions are made? 

B. What actions can produce the greatest benefits (both in time and areal extent)? 

C. What actions are needed to reduce the amount of contaminated dredged 

material from about 70% in year 2000 to less than 15% by 2040? (These are the 

targets set in the Army Corps of Engineers’ (COE) Dredged Material Management 

Plan for the harbor.) 

3

Testing of harbor dredged materials proposed for open water disposal has revealed that 

many sediments contain contaminants that are bioaccumulated by organisms (i.e., clams, 

Macoma sp., and worms, Nereis sp.). In addition, many sediments have been found to be 

acutely toxic to amphipods in laboratory tests. The primary contaminants of concern are 

PCBs, dioxin, polycyclic aromatic hydrocarbons (PAHs), DDT (and its metabolites), 

chlordane, cadmium and mercury. As CARP has progressed, other contaminants have 

been added to the list of contaminants of concern. The current list of analytes to be 

measured by CARP is contained in Table 1. 

Research and development of a contaminant fate and transport model to assess the 

effects of various organic contaminant loads on the ecosystem (including sediments) was 

initiated during 1995. This effort, undertaken by researchers at Manhattan College, was 

sponsored by the Hudson River Foundation (HRF) with co-funding from the Port Authority 

of New York and New Jersey (Port Authority) and EPA. The resulting large-space-scale, 

seasonal-time-scale model for contaminant fate and bioaccumulation is relevant to 

dredged material management since it can be used to address the above questions by 

assessing the effects of contaminant loads on dredged material endpoints such as the 

bioaccumulation of PCBs, dioxin and PAHs. 

Currently, this and other similar models have limited utility to dredged material 

management primarily because ambient concentration and loading data for the 

contaminants of concern do not exist. These ambient data are needed to validate and 

verify the model, while the loading data are essential inputs to the model. This shortcoming 

is being addressed by the comprehensive monitoring programs being undertaken by both 

the New York Department of Environmental Conservation and the New Jersey Department 

of Environmental Protection with support from the Port Authority. 

Another limitation of the Manhattan College model stems from its coarse segmentation. 

Finer spatial scaling is needed to provide more information about effects of particular 

dischargers and specific dredging sites. Future models will also have to include other 

problematic chemicals such as DDT (and its metabolites), mercury, cadmium and 

chlordane. And eventually they will need to consider toxicity as well. 

III. 

General Modeling Approach 

To best assist the Port Authority and other dredged material managers, the CARP 

Modeling Work Group has proposed that a tiered process be undertaken for future 

modeling. The first tier involves selecting, refining and applying existing large-space-scale, 

seasonal-time-scale model(s) for contaminant fate and bioaccumulation. The model(s) 

must be an advancement over previously constructed models to incorporate: (1) all of the 

primary contaminants of concern (i.e., PCBs, dioxin, PAHs, DDT, mercury, cadmium and 

chlordane); (2) appropriate spatial coverage in New York Harbor to evaluate dredging sites 

and the influence of “hot spots”; and (3) appropriate water, suspended sediment and 

organic carbon kinetics. The model(s) will then be run using newly collected monitoring 

4

data provided by both states to obtain preliminary answers to those questions listed above. 

Such analyses will highlight dominant sources, sinks and transport pathways for Harbor 

contaminants, and predict trends in terms of dredged material endpoints. Also, these 

analyses may identify potential data deficiencies in the States’ ongoing monitoring plans. 

The first-tier modeling results, anticipated in approximately two years, will be used to 

develop priorities for contaminant reduction actions, to update the DMMP for the Port, and 

to assist the region in planning for future port development. 

The second tier of the modeling effort involves the development of explicit, finer-scale 

models that couple hydrodynamics, water quality, and cohesive sediment transport. These 

models can be used to guide and implement geographically specific reduction strategies 

and dredged material management. Potential regulatory actions to reduce contamination 

(e.g., TMDLs) will likely require assessments at very fine spatial and temporal scales, 

including assessments of effects of individual discharges on the concentrations of 

contaminants in various media at specific areas of the Harbor. Since water quality criteria 

are at issue with regard to TMDLs, it may be necessary to assess these impacts on a 

monthly, daily or even hourly basis. This is in contrast to current dredged material endpoints 

(i.e., bioaccumulation and toxicity) which may be tracked at yearly intervals. 

Dredged material managers have expressed the need to assess the accumulation of 

contaminated sediments in specific navigation channels and berthing areas throughout 

New York Harbor. They are particularly interested in understanding the relation between 

erosion in certain shoal areas to deposition and contamination of nearby channel areas. 

Developing the predictive understanding of these processes will require an explicit finescale 

cohesive sediment transport model(s) to be constructed and a database of sitespecific 

sediment characteristics to be compiled. This is a large and complicated 

undertaking but can be combined with the fine-scale hydrodynamic and water quality model 

development described above. 

In summary, Tier-1 modeling will provide crucial planning information for the design of 

regional contaminant reduction programs, and will inform both dredged material managers 

and the public of the likely improvements to sediment, water and biota quality resulting from 

reduction actions. It is proposed that this task be completed within a timeframe of eighteen 

months to two years, depending on the availability of monitoring data. Tier-2 will provide 

fine-scale modeling methods to support very specific contaminant reduction actions where 

further detailed information is required. The fine-scale modeling effort may be completed 

within three to four years. 

5

Pesticides 

Hexachlorobenzene 

alpha HCH 

beta HCH 

gamma HCH 

Heptachlor 

Aldrin 

Oxychlordane 

gamma-Chlordane (trans-) 

alpha-Chlordane (cis-) 

o,p'-DDE 

p,p'-DDE 

trans-Nonachlor 

cis-Nonachlor 

o,p'-DDD 

p,p'-DDD 

o,p'-DDT 

p,p'-DDT 

Mirex 

Heptachlor Epoxide 

alpha-Endosulphan (I) 

Dieldrin 

Endrin 

beta-Endosulphan (II) 

Endrin Aldehyde 

Endosulphan Sulphate 

Endrin Ketone 

Methoxychlor 

PCBs 

All 209 congeners (in 

159 domains) for the 

New York program; a 

somewhat abbreviated 

list to be determined 

for the New Jersey 

program 

Dioxin/Furans 

2,3,7,8-TCDD 

1,2,3,7,8-PeCDD 

1,2,3,4,7,8-HxCDD 

1,2,3,6,7,8-HxCDD 

1,2,3,7,8,9-HxCDD 

1,2,3,4,6,7,8-HpCDD 

OCDD 

2,3,7,8-TCDF 

1,2,3,7,8-PeCDF 

2,3,4,7,8-PeCDF 

1,2,3,4,7,8-HxCDF 

1,2,3,6,7,8-HxCDF 

1,2,3,7,8,9-HxCDF 

2,3,4,6,7,8-HxCDF 

1,2,3,4,6,7,8-HpCDF 

1,2,3,4,7,8,9-HpCDF 

OCDF 

Heavy metals 

Total Mercury 

Total Cadmium 

Dissolved Methyl Mercury 

Dissolved Mercury 

Dissolved Cadmium 

Dissolved Lead 

Other 

Total Suspended Solids 

Dissolved Organic Carbon 

Particulate Organic Carbon 

Table 1: CARP Analyte List 

PAHs 

Naphthalene 

Acenaphthylene 

Acenaphthene 

Fluorene 

Phenanthrene 

Anthracene 

Fluoranthene 

Pyrene 

Benz[a]anthracene 

Chrysene 

Benzo[b,j,k]fluoranthene 

Benzo[e]pyrene 

Benzo[a]pyrene 

Perylene 

Dibenz[a,h]anthracene 

Indeno[1,2,3-cd]pyrene 

Benzo[g,h,i]perylene 

C1 Naphthalenes 



C1 Phenanthrenes/Anthracenes 

6

IV. 

Geographic Scope 

The models will be used to develop contaminant reduction plans for the NY/NJ Harbor, with 

specific attention paid to dredged material and TMDL development. The domain of the model 

will need to encompass the area known as the NY/NJ Harbor. The NY/NJ Harbor Estuary 

Program (HEP) identifies the Core area of the NY/NJ Harbor: 

“as the waters from the Sandy Hook/ Rockaway transect to the Hudson River at the 

Tappan Zee Bridge including the following water bodies: the Lower New York Bay; the 

Jamaica Bay; the Sandy Hook Bay; the Raritan Bay; the Raritan River to the 

Fieldville Dam; the Arthur Kill; the Kill van Kull; the Upper New York Bay; the Newark 

Bay; the Passaic River to the Dundee Dam; the Hackensack River to the Oradell 

Damn; the East River to the Throgs Neck Bridge; and the Harlem River.” 

The models must take into account boundary conditions and loading from major tributaries, 

including the Elizabeth River, Woodbridge Creek, Rahway River, to the above water 

bodies. The model should extend into the Bight Apex, the Long Island Sound beyond the 

Throgs Neck Bridge and the tidal Hudson River to the Troy Dam, as necessary, to allow a 

better understanding of boundary conditions at these important sites. The modeling effort 

should use site-specific local area data to the maximum extent practicable. 

V. Local Study Area Features 

Spatial distributions of mercury concentrations, Total PCBs and Total PAHs in Harbor 

sediments are displayed in Figures 1-3, as compiled in the recent U.S. EPA, Regional 

Environmental Monitoring and Assessment Program (R-EMAP) (Adams et al., 1998). 

Sediment mercury concentrations that exceed the 0.71 ppm Effects Range-Median (ERM) 

concentration occur primarily in portions of Upper Bay, Newark Bay, The Kills and extend 

into southern Raritan Bay (Figure 1). Similar spatial patterns are reported for Total PCBs 

(Figure 2), though highest levels occur in the upper Hudson River Estuary. Total PAH 

concentrations follow a similar pattern (Figure 3), although maximum Total PAHs are 

typically below the ERM. These patterns are consistent with findings of relatively low 

survival rates in Newark Bay for the test amphipod, Ampelisca abdita (Adams et al., 

1998). 

The contaminants of concern typically bind preferentially to carbon-rich, fine-grain 

sediments such as fine silts and clays. The average percent silt-clay in Harbor sediments 

is 35% (Adams et al., 1998). Newark Bay is the muddiest basin with 68% silt-clay; Lower 

Harbor is the sandiest, with only 26% silt-clay. Representative physical parameters of 

Harbor sediments are listed below in Table 2: 

7

Table 2: Sediment Physical Parameters (reproduced from Adams et al., 1998) 

Harbor Jamaica 

Bay 

Newark 

Bay 

Lower 

Harbor 

Upper 

Harbor 

W. L.I. 

Sound 

% silt-clay 34.8 30.3 68.1 26.8 51.0 63.2 

+6.1 +9.7 +8.6 +8.8 +10.1 +10.5 

%TOC 1.9 1.9 2.3 1.7 2.5 2.3 

+0.3 +0.7 +0.6 +0.4 +0.5 +0.7 

Bight 

Apex 

7.7 

+3.4 

1.2 

+0.4 

Hydrophobic organic contaminants such as PCBs have a strong affinity to sorb onto both 

particulate and dissolved organic carbon. The average Total Organic Carbon (TOC) in 

Harbor sediments ranges from 1.7% to 2.5 % (Adams et al., 1998). No significant 

differences in %TOC were found among Harbor basins. However, there are no sites in 

Newark Bay where the TOC is less than 0.5%. 

Within the upper Hudson River Estuary (from Hudson to Kingston), bottom sediments are 

generally coarse but become finer southward (Coch, 1986). From Kingston southward to 

the Tappan Zee, the bottom is covered by distinctly finer and uniform sediment facies. 

Grain size coarsens steadily south of the Tapan Zee (Coch, 1986). However, there is 

significant heterogeneity in all areas of the Estuary (H. Bokuniewicz – personal 

communication). 

VI. 

Available Bi-State Monitoring Data 

The proposed modeling tasks will be limited, in part, by the spatial and temporal resolution 

of the available monitoring data. An overview of such resolution in the NYSDEC and 

NJDEP sampling programs is provided in Tables 3a-3b and 4a-4c, respectively. As 

indicated, the NYSDEC sampling is being conducted primarily at seasonal time scales 

and large spatial scales. This was recommended by the CARP Work Group so that the 

data would be usable and consistent with segmentation in the Tier-1 models described 

above. In contrast, the NJDEP plan provides: (1) continuous measurements (for selected 

periods of time) of various hydrodynamic variables (tides, currents, conductivity, 

temperature, suspended sediment); (2) primarily event-based sampling for toxic 

constituents along selected cross-sections and transect centerlines; and (3) a spatial focus 

on the Newark Bays/Kills Complex and selected tributaries. Thus, the NYSDEC’s ambient 

and loading data will be most amenable to the requested Tier-1 tasks. The NJDEP’s data 

will augment the NYCDEC’s data in support of certain Tier-1 tasks (e.g., compiling loads 

from New Jersey’s dischargers, CSOs, SWOs and head-of-tide tributaries) and provide 

additional spatial and temporal resolution within the Newark Bay/Kills Complex. 

8

MATRIX 

Table 3a. Summary of NYSDEC ambient water, sediment, and biota sampling plan 

NUMBER OF 

STATIONS 

SAMPLING 

FREQUENCY 

PARAMETERS 

Near-Bottom Water 

Column 

30 seasonal (3-4 times per year) Dissolved & particulate 

concentrations, DOC, POC, TSS, pH, S 

Near-Surface 

18 

4 occasions PCBs, pesticides, PAHs 

Water Column (including boundaries) 

Sediment Cores 40 once (for initial conditions) Particulate concentrations, DOC, POC, grain sizes, 

AVS, radio tracers 

Zooplankton 9 Tows once during spring PCBs, dioxin, furan, PAHs, Hg, Cd, etc. 

Benthic Invertibrates 8 Seasonal PCBs, dioxin, furan, PAHs, Hg, Cd, etc. 

Fish/Crustaceans 8 areas Seasonal PCBs, dioxin, furan, PAHs, Hg, Cd, etc. 

Table 3b. Summary of NYSDEC Contaminant loading sampling plan (excluding trackdown monitoring) 

LOADING SOURCES 

SAMPLING FREQUENCY 

All STPs 

~6 STPs 

once per year (summer) 

2 dry-weather; 2 wet-weather 

20 Industrial Dischargers 

~3 Industrial Dischargers 

15 CSOs 

3 CSOs 

5 Major Tributaries 

3 Minor Tributaries 

Air Monitoring (research being conducted by Dr. Steven 

Eisenreich, Rutgers U., will be used to quantify air deposition) 


seasonal (4 times per year) 

15 STP influent samples 

seasonal (4 times per year) 


4 times 

at least 3 sampling sites 

collections at one to two-week intervals 

20 Stormwater Outfalls once per year (summer) 

5 Landfills 10 leachate and 25 runoff samples 

9

Table 4a. Summary of New Jersey ambient monitoring plan for Newark Bay/Kills Complex 

SAMPLING 

LOCATION 

Confluence of Passaic and 

Hackensack Rivers, 

Bayonne Bridge, Goethals Bridge 

SAMPLING 

INTERVAL 

SAMPLING 

FREQUENCY 

PARAMETERS 

30-day periods continuous Tidal elevations, vertical current profile, suspended 

sediment concentration, particle size distributions 

conductivity and temperature 

Perth Amboy and Constable Hook 30-day periods continuous tidal elevations 

Transects within Complex 

Event based (six 

transects per 

event) 

same as for tributary and HOT 

sampling (Table 3c), 

depending on where events 

occur 

Table 4b. Summary of New Jersey discharge monitoring plan 

SAMPLING 

LOCATION 

SAMPLING 

INTERVAL 

SAMPLING 

FREQUENCY 

cross-sectional profiles of velocity, SS, sediment size, 

conductivity and temperature; cross-sectional averaged 

PCBs, Pesticides, Dioxins/Furans, (and surrogates of 

above); transect centerline samples of PAHs, Hg, Cd, 

TSS, DOC, POC; 

PARAMETERS 

11 POTWs Seasonal 

(3-4 times) 

TOPS (time-integrated) and/or 

grab (instantaneous) 

PCBs, Pesticides, Dioxins/Furans, (and surrogates of 

above); PAHs, Hg, Cd, Pb; and TSS, DOC, POC 

Selected CSO and SWO sites Concurrent wet-weather grab (instantaneous) PCBs, Pesticides, Dioxins/Furans, (and surrogates of 

(40 samples) 

events 

above); PAHs, Hg, Cd, Pb; and TSS, DOC, POC 

Targeted Industrial Facilities (3-4 times) Targeted subset of list 

Table 4c. Summary of New Jersey tributary monitoring plan 

SAMPLING 

LOCATION 

Head-of-Tide (HOT) Tributaries 

(Passaic, Hackensack, Raritan, 

Elizabeth and Rahway Rivers) 

SAMPLING 

INTERVAL 

2 dry-weather periods, 4 wetweather 

events, 1 contingent 

event, 1 “extra” 

SAMPLING 

FREQUENCY 

Up to 1 sample unit* at 

each of 5 tributary HOT 

stations per event 

PARAMETERS 

Streamflow, PCBs, PAHs, Pesticides, Dioxins/Furans, 

(and surrogates of above); Hg, Cd, Pb, PAH; TSS, DOC, 

POC 

Tidal Tributary regions 

(Raritan/Elizabeth/Rahway 

And Passaic/Hackensack) 

one tributary region monitored 

per event 

Passaic R. (3 sites) 

Hackensack R. (3 sites) 

Raritan R. (2 sites) 

Elizabeth R. (1 sites) 

Rahway R. (1 sites) 

10 

PCBs, PAHs, Pesticides, Dioxins/Furans, (and 

surrogates of above); Hg, Cd, Pb, PAH; TSS, DOC, 

POC;cross-sectional profiles of velocity, suspended 

sediment, sediment size, conductivity and temperature 

*1 sample unit consists of 1 TOPS/XAD sample of PCBs and pesticides; 1 TOPS filter sample of PCBs, pesticides, dioxins/furans and PAHs; 1 grab 

sample of TSS and PAHs; and 1 grab sample of Hg, Cd, and Pb

VII. 

Tier-1 Modeling Tasks 

As noted above, the overall goal of the Tier-1 modeling effort will be to develop priorities 

for contaminant reduction actions, update the DMMP, and to assist the Port Authority in 

future Water Resources Development Act planning. Towards these objectives, the 

following modeling tasks are requested: 

Task 1-1: The first task will be to select a large-space-scale, seasonal-time-scale model(s) 

for contaminant fate, transport and bioaccumulation. It is envisioned that three 

formulations of existing models will be further refined and developed for 

hydrophobic organics, inorganic metals and mercury. The proposed Tier-1 

modeling can either build upon the Thomann-Farley Model (WASTOX; Connolly, 

1991; Connolly and Thomann, 1985), or it can recommend other appropriate 

models. In either case, a full justification for selection should be given in the 

proposal. 

Simulated fate and transport processes for the water column should include 

effects of advection, dispersion, external sources, settling, resuspension, bed 

diffusion, volatilization and aerobic degradation. Likewise, coupled sub-models 

for the sediment layers should compute variations in sediment contaminant 

concentrations due to settling, resuspension, burial, transformations, sedimentwater 

column diffusion, and diffusive exchange with deep sediments. In 

modeling the hydrophobic organic contaminants of concern, chemical 

partitioning between freely dissolved and particulate phases may be assumed to 

be functions of the fraction of organic carbon on the solids and the octanol-water 

partitioning coefficient (Karickhoff, 1981). PCBs should be modeled as PCB 

homologue groups or other congener groupings rather than total PCBs. The 

modeling and data analysis, however, must be capable of resolving PCB 

predictions into total PCB concentrations to be compared with existing 

endpoints. 

The modeling framework should include either a bioconcentration factor or, 

preferably, a coupled food-chain model to calculate the accumulation of 

contaminants in biota. The various species being collected and monitored for 

contaminant levels are listed in Table 5. The model(s) must be capable of 

predicting concentrations of the primary contaminants of concern (i.e., PCBs, 

dioxin, PAHs, DDT, cadmium, mercury and chlordane) in polychaete worms 

(Nereis sp., or an appropriate surrogate) and clams (Macoma sp., or 

appropriate surrogate). Biota-Sediment-Accumulation-Factors (BSAFs) may 

be employed for calculating contaminant concentrations in these dredgedmaterial 

test organisms. The model(s) must also be capable of evaluating and 

predicting uptake of the primary contaminants in up to four higher trophic level 

species (striped bass, white perch, American eel and blue crab). Proposers 

must discuss the limitations in knowledge for modeling all four species, and 

recommend which species can be readily modeled to provide the most 

11

scientifically reliable results. 

Task 1-2: The second task is to refine the selected model(s), as appropriate, to ensure that 

the following features are included: 

• Appropriate spatial resolution in model segmentation, especially in the 

vicinity of known hot spots and dredging areas 

• Salinity calibration for both spring and fall seasons 

• Incorporation of site-specific atmospheric deposition data into the model and 

formulations to account for air-water exchange of contaminants that can be 

linked to other atmospheric transport models and /or other regional research 

efforts 

• Upgraded organic carbon kinetics 

• The inclusion of the biota components described in Task 1-1 

Also, the following optional model refinements are recommended: 

• Added vertical layer(s) to water column 

• Refined partitioning formulations, where appropriate 

• Refined solids balance component 

Task 1-3: Review and compile recent baseline data for the Harbor, including: 

• Harbor bathymetry 

• Harbor sediment grain-size distributions 

• Sediment contaminant distributions (i.e., PCBs, dioxin, PAHs, DDT, Mercury 

and chlordane) 

• Sediment %TOC distributions 

• Sediment erodibility characteristics (e.g., erosion rates, critical shear stresses), 

if available. This will be necessary for Tier-2 modeling. 

Sources for this information include those cited in Section V of this RFP as well 

as the following: the IT corporation, Battelle Systems, Manhattan College, the 

U.S. Army Corps of Engineers and NOAA. Based on this review, a background 

narrative should be prepared to characterize observed spatial and temporal 

trends in these data – including trends and features that should be reproduced by 

the requested model. 

Task 1-4: Compile new/updated loading estimates for all the contaminants listed in Table 

1. Compare relative loading contributions of the various point and nonpoint 

source categories in tabular and graphical (e.g., pie chart) formats, suitable for 

public presentations. To the extent possible, provide estimates of the 

uncertainty associated with each loading estimate. 

Task 1-5: Using the available CARP monitoring data, conduct calibrations/verifications for 

PCBs, PAHs, Dioxin, DDT, Mercury, cadmium and Chlordane. Prepare flux 

balance diagrams for each season to identify dominant flux compartments 

12

Table 5. Biota Sampling to be conducted by NYSDEC 

Species 

Total Samples 

(Projected) 

White Perch 360 

Striped bass 360 

Winter Flounder 360 

Mummichog 72 

Polychaete 54 

Shrimp/Amphipod 54 

Zooplankton 45 

Bivalve 216 

Cormorant Eggs 40 

Cormorant Blood 40 

Cormorant Plasma 40 

Cormorant Feathers 40 

Cormorant Down 40 

Blue Crabs 135 

American Eel 108 

Sampling Locations 

Hudson River at Poughkeepsie 

Hudson River at Haverstraw Bay 

Upper New York Bay 

Newark bay 

Passaic River 

Raritan Bay 

Jamaica Bay 

NY Bight 

Long Island Sound at Eatons Neck 

13

Task 1-6: Conduct model sensitivity runs to estimate effects of uncertainties in model inputs 

on simulated contaminant concentrations and mass balances. In particular, effects 

of uncertainties in the compiled loading data (Task 1-3) should be evaluated. 

Task 1-7: Conduct model scenario analyses to assess the following: 

• Current status of Harbor water quality and sediment quality with respect to 

dredged materials end points and levels of the primary contaminants of concern 

in the biota (Macoma sp., Nereis sp., and the other species selected for 

modeling). 

• Time History/projections for the anticipated timeframe required for safe ocean 

placement of dredged materials at the HARS. To this end, results of the 

chemical fate model should be used to define test organism (Macoma sp., 

Nereis sp.) exposure concentrations (e.g., test organism concentrations 

computed as the product of sediment contaminant concentrations and chemicalspecific 

BSAFs). The resulting test organism concentrations will then be 

compared to relevant contaminant concentration guidelines at various Harbor 

locations. 

• Time History/projections for contaminant concentration reductions in water, 

sediment and biota related to other regulatory endpoints. At a minimum, the 

model should be used to compute the anticipated timeframe required for 

compliance with relevant FDA limits for the consumer species selected for 

modeling. 

• Component load analyses to determine relative effects, on sediments and biota 

(Macoma sp., Nereis sp. and the other biota selected for modeling) of various 

contaminant loading sources, including tributary inflows, WWTPs, industrial 

dischargers, CSOs, SWOs, atmospheric deposition and initial bed deposits. 

• Development of a list of problematic regions (i.e., model segments) and the 

source types most likely to be contributing to exceedences of water quality 

standards, the unacceptability of dredged materials for placement at the HARS 

and contamination in the biota in these regions, as they related to the seven 

primary contaminants of concern. Graphical displays (e.g., GIS output) will be 

developed for public presentation of findings. 

• Model simulations of reductions of contaminant loadings to each of the 

identified problematic regions (i.e., model segments). The goal of these 

scenarios will be to simulate the potential benefits of reducing dominant sources 

(e.g., major dischargers) that are contributing to contamination in these regions. 

The benefits should be evaluated in terms of dredged material end points and 

14

levels of contaminants of concern in the biota (Macoma sp., Nereis sp., and 

other species selected for modeling). 

• Model simulations of the interactions of “hot-spot,” in-place, contaminated 

sediments with water, sediment and biota of the Estuary. The goal of these 

scenarios will be to evaluate these selected Harbor areas as contaminant sources 

to other areas of the Harbor and to evaluate the burial or further contamination of 

these sediments in the future. 

• Time History/projections for improvements in newly deposited sediment quality 

after the simulated contaminant reductions are made or dredging is conducted, 

as specified above. Of particular interest is the minimum timeframe required for 

a reduction in the amount of contaminated dredged material to 15% by the year 

2040. 

Task 1-8: Develop a windows-based user interface for simulating additional scenarios with 

both the chemical fate and bioaccumulation models. This interface will 

incorporate the calibrated fate and transport models, and provide windows 

dialog boxes for prescribing alternate combinations of external loads and 

species-specific parameters (e.g., % lipid, age class, trophic level, egestion and 

excretion rates, etc.). Also, a post-processor will be developed to store and 

display the model results in a GIS-compatible format. 

Task 1-9: Develop a modeling approach to evaluate sediment toxicity. Many of the 

sediments of New York Harbor have been shown to exhibit unacceptable toxicity 

to amphipods (Ampelisca sp.) through laboratory testing. While the causes of 

the toxicity have yet to be specifically linked to any particular contaminant or 

suite of contaminants, research results from this region and from other systems 

may be useful in formulating conceptual and mathematical models of toxicity. 

For instance, narcosis based upon PAH contamination may be a way of 

evaluating and predicting toxicity. 

VIII. 

Tier-2 Modeling Tasks 

As noted above, the goal of the Tier-2 modeling effort will be to develop explicit, finer-scale 

models that couple hydrodynamics, water quality, and sediment transport, and that can be 

used to guide and implement geographically specific reduction strategies and dredged 

material management. Because there may be several viable approaches to achieve this 

goal, the Tier-2 tasks will be more open-ended than Tier-1 tasks. Nevertheless, all 

possible approaches should build on existing knowledge and databases. 

Task 2-1: Develop a Tier-2 model(s) that includes the following fully linked components and 

qualities: 

• Water Quality Model (including carbon kinetics) 

• Hydrodynamic Model: updatable to take into account changes in Harbor 

15

athymetry, variable flows, fixed flows, and critical period. 

• Sediment Transport Model: linked and functional sediment transport model 

• A Linked Wind-Wave Model to support the sediment transport simulations 

• Bioaccumulation Model: updated from Phase 1, as necessary. 

• An air-water transport component that can be linked to other appropriate air 

deposition models 

In Addition, the models must: 

• Be technically sound and legally defensible. 

• Pass the scrutiny of an unbiased Modeling Evaluation Group (MEG). 

Proposers are to provide a rationale for the selection of an appropriate spatial 

and temporal resolution for the finer-scale (Tier-2) hydrodynamic and water 

quality models. This rationale must include consideration of available 

monitoring data, relevant physical and biogeochemical processes, and the 

need to address key management issues such as: 

• Source trackdown 

• Localized source reductions 

• Hot Spot dredging 

• Water quality criteria 

• TMDLs 

• Predicting sediment deposition in channel/berthing areas 

Proposers must provide a rationale for their preliminary selection of each of the 

model components prescribed above. List all of the important features, 

capabilities and advantages of each model. The proposer should describe 

their previous applications of these models and their applicability to the present 

study. 

It is recognized that some of the model components require further research 

and development before they can be fully applied to management scenarios, 

particularly the sediment transport component. Therefore, proposers must 

discuss key limitations of each of the proposed model components in terms of 

their formulations, data requirements, research requirements and the issues 

listed in Task 2-2. Indicate how your model development will overcome and/or 

factor in these limitations. 

For example, is the predictive ability of the proposed toxics model limited by 

assumptions regarding rapid and reversible equilibration between the liquid 

and solid phases? How will numerical dispersion be minimized in the water 

quality model? How can the different sampling schemes employed by 

NYSDEC and NJDEP be utilized effectively? 

16

Likewise, can the sediment transport model be truly predictive without detailed, 

site-specific information regarding sediment erosion rates and critical shear 

stresses? If not, how will the proposed program eliminate this potential 

deficiency? How will the sediment transport model simulate complex 

processes such as aggregation and break-up of cohesive suspended 

sediments? How will bioturbation be handled? 

Describe, in as specific terms as possible in your proposal, how the selected 

Tier-2 models can be applied to address the issues of concern; namely, 

TMDLs, water quality standards, source reductions, hot spot dredging, etc. 

Task 2-2: Review the adequacy of the sampling designs in the New Jersey and New 

York Toxics Reduction Workplans and identify how they should be modified to 

optimize the modeling effort. Also, recommend what additional monitoring is 

needed to accommodate the prescribed Tier-2 model(s) so that additional costs 

may be estimated. 

IX. 

Model Application 

Task 3-1:Develop user manuals for applyingTier-1 and Tier-2 models and working with 

associated model products (e.g., GIS outputs). Such manuals should be userfriendly 

documents that can be used by the States and EPA in the development of 

TMDLs. 

Task 3-2: Provide training to CARP participants on the use of the both models and 

associated products. It is anticipated that training sessions will be needed at sites 

in Trenton, NJ, Albany, NY, and New York City. 

Task 3-3: Provide a recommendation and cost estimate for long term maintenance of the 

models. 

X. Summary of Desired Model Features 

The Tier-1 and Tier-2 models will need to be assessed by (and available for use by) 

modeling professionals in both States, the NY District Corps of Engineers, and the USEPA 

for various program-specific work consistent with the above listed goals. 

The Tier-2 model must take into account, at a minimum, the following technical areas: 

hydrodynamic transport, primary productivity, organic carbon kinetics, sediment transport, 

hydrophobic chemical fate and transport, trace metals fate and transport, Mercury fate and 

transport, and bioaccumulation and food chain dynamics. The spatial and temporal scale 

of the model must be sufficient to address compliance with appropriate standards/criteria 

in water, sediment and biota. 

17

Both models will use loadings information (to be obtained from the State’s Toxic 

Workplans and other sources) for the following source categories: 

• Major Tributaries 

• Major Rivers 

• Atmosphere 

• Combined Sewer Overflows (CSOs) / Stormwater 

• Municipal Discharges 

• Industrial Discharges 

• Sediments, including hot spots 

• Non-point land-based sources 

The Tier-1 and Tier-2 models should be flexible and user-friendly, and accessible/run from 

a Windows-based platform. The models’ source codes should be available to the States, 

EPA and other Agencies involved in this program. The models must have the capability to 

predict impacts on water quality, sediments, and biota resulting from point and nonpoint 

source discharges; thus, they should have the ability to be linked to land-side models, 

including run-off, air deposition and CSO models, and a GIS platform. 

The Tier-2 model will be a state-of-the-science product at the time of its completion. It will 

likely, however, be limited in some aspects because of scientific uncertainties in fully 

understanding fate, transport and effects of contaminants. The modeling should be viewed 

not only as an interim management tool, but as a research tool from which fuller 

understandings of the of fate and transport of contaminants can be gleaned. In addition, 

the model can serve as the framework for more advanced models to be developed in the 

future that can applied to new and emerging management issues. Therefore, the model 

and its codes, must be available to the scientific community and proposers are 

encouraged to suggest processes for linkages and collaboration with other scientists and 

engineers in order to accomplish this goal. 

The models will be subject to the review and approval by a Model Evaluation Group (MEG). 

The MEG will provide feedback to the CARP, and to the contractor on the acceptability of 

modeling concepts, model calibration, validation, precision and accuracy. 

XI. 

Summary of Deliverables 

A. Quarterly Progress Summaries 

Quarterly progress summaries are required starting from the contract execution date. 

The summaries should discuss the work accomplished during the reporting period, the 

status of current work, updated project schedule, problems or delays experienced 

during the reporting period, and actions being taken to rectify problems, activities 

projected over the next reporting period. The Contractor must submit ten copies of 

each quarterly summary. 

18

B. Final Reports 

Final reports will be due in accordance with the agreed upon schedule contained in 

the eventual contract. Each modeling tier will have a separate final report. Draft final 

reports will be reviewed by HRF, along with CARP, with written comments submitted 

back to the Contractor. The Contractor must submit twenty copies of the draft and final 

reports. The model and source codes for Tier-1 and Tier-2 models will be included in 

the final reports. 

C. Meetings 

Periodic meetings will be required throughout the term of the contract to meet with 

CARP representatives to review modeling progress and to seek input from the 

modeling contractor on other elements of CARP. Most of these meetings will be 

convened at the Hudson River Foundation offices. 

Training on how to use the model will be provided at up to three locations. 

XII. 

Schedule 

All Tier-1 modeling tasks are to be completed within a two-year period. The requested 

Tier-2 tasks are to begin immediately and completed within a four-year period. Proposers 

should submit a detailed schedule. 

XIII. Communication, Coordination and Other Requirements 

The Contractor's sole contact for all contract related matters during the course of this 

project will be the Hudson River Foundation. However, communication between the 

Contractor and all relevant CARP investigators and managers is strongly encouraged. The 

Contractor will receive all contract orders and approvals from the Hudson River Foundation 

who, in turn, will work closely with CARP managers. 

Financial resources for model development are being provided to the Hudson River 

Foundation by the Port Authority of New York and New Jersey as part of the Joint Dredging 

Plan for the Port of New York and New Jersey. The requirements and conditions of the 

agreement between the Port Authority and the Foundation are applicable to any 

contractors the Foundation selects to perform services in connection with that agreement. 

Such requirements and conditions will be included in contractual arrangements between 

the Foundation and the modeling contractor. 

Submission Requirements: 

Please refer to the Instructions sheet for more information about submission requirements. 

19

Twenty Copies of the Proposal should be sent by the close of business on September 8, 

2000 to: 

Dr. Dennis Suszkowski 


40 West 20 th Street, 9 th Floor 

New York, NY 10011 

20

References 

Adams, D.A., O’Connor, J.S., and Weisberg, S.B. (1998). “Sediment Quality of 

the NY/NJ Harbor System: An Investigation Under the Regional Environmental 

Monitoring and Assessment Program.” EPA/902-R-98-001. 

Coch, N. (1986). “Sediment Characteristics and Facies Distribution in the Hudson 

System.” North East Geology. 8:109-129. 

Connolly, J.P. (1991b). “Users Guide for WASTOX2, Version 2.51.”, Manhattan 

College, Riverdale NY. 

Farley, K.J., Thomann, R.V., Cooney, T.F., Damiani, D.R., and Wands, J.R. 

(1999). “An Integrated Model of Organic Chemical Fate and 

Bioaccumulation in the Hudson River Estuary.” Prepared for the Hudson 

River Foundation for Science and Environmental Research. Manhattan 

College, Riverdale, New York, 169pp. 

Karickhoff, S.W. (1981). “Semi-empirical estimation of sorption of hydrophobic 

pollutants on natural sediments and soils.” Chemosphere, 10(8), 833-846. 

TAMS/Gradient. (1995). “Further Site Characterization and Analysis Database 

Report. Phase 2 Report – Review Copy.” EPA Contract No. 68-S9-2001, 

U.S. Environmental Protection Agency, Region II. 

21

Figure 1: Distributions of sediment mercury concentrations (Reproduced from Adams et al., 1998) 

22

Figure 2: Distributions of sediment PCB concentrations (Reproduced from Adams et al., 1998) 

23

Figure 3: Distributions of sediment PAH concentrations (Reproduced from Adams et al., 1998) 

24

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