Habitat Restoration Plan for the Lower Tuolumne River Corridor ...

7Natural channel processes...The foundation of a river ecosystem is the dynamic interactionof flowing water, sediment, and riparian vegetation.Alteration of one of these factors disruptsthe balance of the other factors. Forexample, clearing riparian vegetation mayincrease bank erosion and channelmeandering. Dams block the downstreammovement of gravel from the upperwatershed, causing gravel bars downstreamof dams to be scoured awaywithout being replaced. Absence of floods allows fine sedimentsto accumulate in gravels, inhibiting the survival ofchinook salmon eggs. These impacts in turn degrade oreliminate important fish and wildlife habitat and reduce theirpopulations.ATTRIBUTE #1Spatially complex channel shape (morphology)No single segment of river provides habitat for all species, butthe sum of different areas of the river provides high-qualityhabitat for native species.“The channel is carved by the flowingwater, but it takes the form dictatedby the sediment carried.”Luna LeopoldAttributes of river ecosystem integrityBased on an historical evaluation of Tuolumne River hydrology(streamflow patterns) and geomorphology (river channelform), and a review of scientific literature, the Attributes ofRiver Ecosystem Integrity were developedto describe how the Tuolumne Riverfunctioned historically, and also to serveas measurable restoration objectives. Bymanaging streamflows, reducing unwantedfine sediment supply, increasingimportant coarse sediment supply, andrestoring a natural channel form, many ofthe critical river attributes and processes can be achieved.This restoration approach focuses on restoring a naturalpattern of periodic disturbance and continual re-growth thatcreates a mosaic of high quality habitat for many species,including salmon. Without these dynamic processes, the riverhas become static and less biologically productive.ATTRIBUTE #3Frequently disturbed riverbed surfaceIn the upper river (from La Grange Dam to Hughson) wherethe river bed is mostly made of gravel, surface gravels andcobbles are moved downstream by moderate streamflowswhich occur on average every 1 or 2 years. In the lower river(from Hughson to the San Joaquin River) where the bed ismostly sand, sand is moved downstream during much of theyear, creating migrating “dunes” and shifting sand bars.ATTRIBUTE #2Variable streamflow patternsSeasonal streamflow patterns are broadly predictable, butspecific flow magnitudes, timing, durations, and frequenciesare unpredictable due to runoff patterns produced by storms,droughts and snowmelt. Streamflow variability is a foundationof river ecosystem health.Streamflow X 1000 (cfs)1098765432101-OctWinterBaseflows1-NovWinterFlood1-Dec1-Jan1-Feb1-Mar1994 Unregulated Streamflows1994 Regulated StreamflowsSpringSnowmelt1-Apr1-May1-Jun1-JulSummerBaseflows1-Aug1-SepATTRIBUTE #4Periodic riverbed scour and fillIn gravel-bedded reaches, larger floods move entire gravelbars, not just their surface layers. These large floods occur onaverage every 3 to 5 years. This “scour” is typically accompaniedby “fill” from upstream gravel sources, which maintains abalance in natural channel form. This process is important forremoving fine sediments from salmon spawning gravels.ATTRIBUTE #5Balanced fine and coarse sediment volumesThe location and volumes of sediment within a river reachmay vary year to year, but over the long term the amount ofsediment entering and leaving the river is balanced, and thechannel form remains similar. A balanced sediment loadimplies that streamflows are periodically high enough to movemost sediment sizes (sand and boulders) in the river.

...the technical aspects of river ecosystemsAn example of the dynamics of naturalrivers is depicted at right. ( A) A channelwith adequate space to migrate (Attribute6) erodes the channel bank onthe outside of the meander bend duringhigh flows (Attribute 2), ( B) encouragingaged riparian trees to topple into thechannel (Attribute 9). ( C) A deep poolalso forms here, which provides structuralcomplexity (Attribute 1) for good fishhabitat. As bank erosion continues, the pool“migrates” downstream (Attribute 6), but highquality habitat is maintained. (D) On the oppositebank, high flows (Attribute 2) scour and redeposit coarsesediments (Attributes 4 and 5), forming a shallow bar on theinside of the meander bend (Attribute 1), and providing cleanspawning gravels. (E) This area, in turn, provides ideal slowwaterrearing conditions for juvenile chinook salmon, as wellas habitat for aquatic insects (fish food), amphibians andreptiles. (F) Progressively higher up thegravel bar surface, a dynamic interplay occursbetween receding water levels during the spring snowmelt(Attribute 2), and the presence of riparian tree seeds (Attribute7). These woody riparian trees are sporadically scoured out(Attribute 8), and those established high enough on the bankare toppled into the channel as the channel migrates backacross the valley (A).8ATTRIBUTE #6Periodic channel migration and/or avulsionThe channel erodes riverbanks, deposits new gravel bars, andestablishes meander patterns based on variable streamflows,valley slope, river channel confinement, sediment supply, andsediment size. In the gravel-bedded reaches, the channelmoves from one location to another by sudden change, leavingmuch of the abandoned channel intact. In the sand-beddedreaches, meanders gradually erode through banks and cut offmeander bends, leaving oxbow lakes and wetlands.ATTRIBUTE #7A functional floodplainEvery one or two years, on average, high streamflows inundatethe lowermost floodplains, deposit silts and sand, and stimulategermination of riparian vegetation. Lower terraces, at aslightly higher elevation than floodplains, are inundated byless frequent floods.ATTRIBUTE #9Self-sustaining, diverse riparian corridorBased on species life history strategies and streamflowpatterns, the riparian plant community is maintained by acontinual cycle of germination, growth, and death. Theriparian community thus contains young and old vegetation,and a diversity of species.ATTRIBUTE #8Infrequent channel resetting floodsSingle large floods (recurring once every 10 to 20 years) causemajor channel changes that rejuvenate riparian processes,form and maintain side channels, and create off-channelwetlands, such as oxbows.ATTRIBUTE #10Naturally fluctuating groundwater tableGroundwater fluctuates on a seasonal and annual basis infloodplains, terraces, and sloughs.

TRivers are resilient ecosystems with enormous capacity forself-rejuvenation. However, given that land-use practices and9 water regulation and diversion will continue, the river cannotrecover in a reasonable timeframe without help. The RestorationPlan recommends several strategies to initiate recovery,such as filling mining pits, introducing spawning gravels,lowering selected floodplains to allow inundation, and replantingnative riparian vegetation. Equally important, floodand gravel management will help re-establish processes tomaintain restored areas and improve other areas.The Restoration Plan recommends general restorationstrategies for different reaches along the river, as well asspecific restoration projects within those reaches. Inherentwith any restoration plan of this scale is some degree ofuncertainty regarding the effectiveness of specific restorauolumneRiver restoration strategiesLong-term restoration recommendationsSAND-BEDDED ZONE (RM 0.0 TO RM 24.0)tion actions. Therefore, an adaptive management programwould require 1) monitoring restoration sites, 2) evaluatingrestoration success against desired conditions, and 3)improving restoration strategies. This will ensure progresstoward recovery goals.Implementation of any restoration project will be subject toprior environment review by local, state, and federal regulatoryagencies. The TRTAC participants recognize thatdecisions affecting the Tuolumne River are influenced bydiverse policies relating to land use, water supply and use,water quality, flood control, fish and wildlife, and recreation,and are not governed solely by habitat considerations.Additionally, the TRTAC recognizes the importance ofcooperation and participation from private landowners, thelocal business community, and the general public.• Restore floodway capacity to 15,000 cfs or greater above Dry Creek and 20,000 cfs or greater below Dry Creek• Reduce urban and agricultural encroachment to create/maintain a 500-2,000 ft or greater floodway width• Remove rip-rap and berms where feasible to restore floodplains and to allow migration within the floodway• Seek conservation easements and/or land acquisitions (especially of flood-prone lands) from willing landowners• Remove exotic plants within riparian corridor and replant native species• Secure protection for existing mature valley oaks and Fremont cottonwoods• Improve water quality by managing urban, agricultural and industrial runoff into the river and into Dry CreekDryCreekMODESTOEMPIRESanJoaquinTuolumneREACH 1 (RM 0.0-10.5)Lower Sand-bedded Reach• Restore off-channel wetlands to increasewildlife habitat• Create vegetative buffer to reduce soil erosionand filter agricultural runoff• Restore functional floodplains and nativeriparian forestsCERESREACH 2(RM 10.5-19.3)Urban Sand-bedded Reach• Increase public awareness of theTuolumne and promote cleanup,restoration and monitoring• Improve Tuolumne River RegionalPark by increasing area ofnative riparian trees• Create and preserve riparianbuffer along urban/industrialzones• Remove trash and debris,eliminate chronic sources ofpollution, and actively prohibitillegal dumpingREACH 3(RM 19.3-24.0)Upper Sand-beddedReach• Preserve existingurban setback fromriver• Create and preserve ariparian buffer alongurban/agriculturalzonesHUGHSONREACH 4In-Channel Gr• Isolate/fill inpredation onbedload tran• Restore a nat• Create and malong urban/

RIVER-WIDE RESTORATION GOALS• Chinook salmon habitat maintained by natural processes, sustaining a viable, naturallyreproducing chinook salmon population• Adequate quantity of high quality gravel, maintained by periodically replacing gravelstransported downstream by high flows• A dynamic river channel, maintained by floods of variable magnitude and frequency thatperiodically initiate critical channel processes• A continuous river floodway and riparian corridor from La Grange Dam to the confluencewith the San Joaquin River• Increased extent of naturally regenerating native riparian stands and decreased extentof exotic plants• Adaptive management program that continually reviews and refines restoration andmanagement activities, and addresses areas of scientific uncertainty that will improve ourunderstanding of river ecosystem processes• Improved water quality through urban and agricultural runoff management programs• Increased public awareness and involvement in the Tuolumne River restoration effortGreat Blue Heron10GRAVEL-BEDDED ZONE (RM 24.0-52.1)• Increase gravel supply throughout the zone and increase the frequency of gravel movement• Reduce fine sediment supply and storage• Restore floodway capacity to 15,000 cfs or greater• Reduce agricultural and mining encroachment to create/maintain a 500 ft or greater coridor width• Remove rip-rap and berms where feasible to restore floodplains and to allow migration within the floodway• Manage flood control releases to initiate bed movement and other dynamic channel processes• Restore a continuous corridor of native riparian vegetation• Improve habitat quality of off-channel wetlands• Seek conservation easements and/or land acquisitions (especially of flood-prone lands) from willing landowners• Remove exotic plants within riparian corridor and replant native species• Introduce alternative grazing strategies to promote riparian regenerationLA GRANGEDAM ❰LAGRANGEWATERFORDRiverHICKMAN(RM 24.0-34.2)avel Mining Reachstream mining pits to reduce bassjuvenile salmon and reestablishsport continuityural river and floodplain morphologyaintain riparian buffer (corridor)agricultural zonesREACH 5 (RM 34.2-40.3)Gravel Mining Reach• Isolate off-channel mining pits toprevent river connection duringfloods up to 15,000 cfs to reducesalmon stranding and bass predationon juvenile salmon• Increase floodway width to at least500 feet• Restore a natural river and floodplainmorphology• Restore and maintain ripariancorridor through gravel miningzonesREACH 6(RM 40.3-46.6)Dredger Tailing Reach• Reconstruct remnantchannel left by gold dredgeroperations to a natural riverand floodplain form• Restore riffles to increasesalmon spawning andrearing habitat• Regrade floodplains toreduce salmon strandingand promote riparianregeneration• Reduce riparian encroachmentonto low flow channel• Reduce grazing impacts topromote riparian regenerationon floodplains• Secure remnant dredgertailings for future restorationREACH 7(RM 46.6-52.1)Critical SpawningReach• Reduce sand input intoriver and storage inriverbed (especially inspawning gravels)• Increase and maintainspawning gravel supply• Restore riffles toincrease salmonspawning and rearinghabitat• Regrade floodplains toreduce salmonstranding and promoteriparian regeneration• Reduce riparianencroachment ontoactive channel• Reduce grazingimpacts to promoteriparian regenerationon floodplains

11Restoration in progressResponding to the FERC Settlement Agreement mandate toimplement ten priority restoration projects by 2005, theTRTAC has received funding for several projects from theCALFED Ecosystem Restoration Program and the CVPIA’sAnadromous Fish Restoration Program (AFRP), implementedby the US Fish and Wildlife Service. The TRTAC has selectedsix projects (Phases I-IV of the Gravel Mining Reach andSpecial Run Pools 9 and 10) which are now in the planningand design phase. The remaining four projects are currentlybeing evaluated.valley oak leavesand acornsOther entities are also proposing or conducting restorationactivities on the Tuolumne River, including the US Army Corpof Engineers, US Fish and Wildlife Service, California Departmentof Fish and Game, Natural Resources ConservationService, East Stanislaus Resource Conservation District,Friends of the Tuolumne, California State Parks, and the JointPowers Authority (City of Modesto, City of Ceres, and StanislausCounty). Several of these projects are illustrated below.SAN JOAQUIN RIVERNATIONAL WILDLIFE REFUGEUS Fish and Wildlife ServiceThis site represents one of the few remainingfloodplains in the San Joaquin basinthat has much of its riparian habitat intact.Since this habitat is critical for resident andmigrant bird overwintering, breeding,foraging, and migration stopover, preservingthis site is essential. USFWS is purchasingthese frequently flooded lands toprotect riparian woodlands, revegetatecleared lands, and manage for wildlife.MODESTOTUOLUMNE RIVER REGIONAL PARKJoint Powers Authority(City of Modesto, City of Ceres, Stanislaus County)This project has been undertaken by the Cities of Modestoand Ceres, and Stanislaus County since 1967 with the visionof creating a continuous river park through the greaterModesto urban area. Approximately 700 acres of riversideproperty have been acquired to create the Park. The JointPowers Authority is now revising the land use plan for thePark, preparing a Master Plan for the Gateway Parcel at theDry Creek confluence, and will soon be implementing avariety of restoration activities within the Park.DryCreekEMPIRESanJoaquinTuolumneCERESHUGHSONGRAYSON RIVER RANCHCONSERVATION EASEMENTNatural Resources Conservation ServiceEast Stanislaus Resource Conservation DistrictCALFED/AFRPThe Grayson River Ranch site, located 5 milesfrom the confluence with the San Joaquin River, issubject to frequent flooding. A partnership ofnon-profit, local, state and federal agencies andgroups are funding a Perpetual ConservationEasement for this land. The Grayson project hasthe potential to become a model for futureconservation of floodplain and riparian habitatson the Lower Tuolumne River. (See p. 14 for amore detailed description.)SPECIAL RUN POOLS 9 AND 10CHANNEL RESTORATIONTuolumne River Technical Advisory CommitteeSRPs 9 and 10 are large in-channel gravel miningpits located in a mile-long reach downstream ofFox Grove County Park. These pits harbor populationsof non-native bass that are known to prey onyoung salmon. Restoration will eliminate basshabitat and increase riparian vegetation. Theseprojects have received funding from CALFED andUSFWS/AFRP, and construction will begin in 1999(see p. 13 for more detailed description).

Restoration TypesFloodway expansion: Provide a wider floodway and restorefloodplains to reduce river confinement, allow natural channelmigration, provide additional flexibility for dam operations toreduce the risk of catastrophic floods, increase riparianvegetation, and improve river habitat conditions.Riparian restoration: Replant riparian vegetation to helppromote natural regeneration, specifically targeting Fremontcottonwood and valley oak species.Channel reconstruction: Rebuild a natural channel shapethat allows gravel movement, channel migration, floodplaininundation, riparian regeneration, and sand/silt deposition onfloodplains.Conservation easements: Preserve riparian areas (especiallyflood-prone lands), while ownership of the land is maintainedby private individuals. Riparian restoration could be implementedwithin the conservation easement.Preservation sites: Preserve sites containing stands ofmature riparian trees.Sand management (fine sediment): Reduce fine sedimentwithin riverbed gravels, by prevention, mechanical meansand/or periodic managed flood releases.Gravel management (coarse sediment): Provide an initiallarge volume of gravel to replace the gravels lost over the pastcentury, then periodically introduce gravel to balance the lossof gravels moved downstream during high streamflows.Additional management approaches: Increase water qualityby controlling urban and agricultural runoff; introducealternative grazing strategies within floodway to promotenative riparian regeneration and reduce bank erosion; introducevegetative buffer strips along the river and withinagricultural and urban lands to reduce soil loss, and todecrease sound, air and non-point source pollution into theriparian corridor.12BASSO ECOLOGICAL RESERVE LAND PURCHASECalifornia Department of Fish & Game, Stanislaus CountyAcquisition of three parcels totaling 42 acres is being funded by CALFED. This land between LaGrange Bridge and Basso Bridge represents the “missing link” connecting adjacent 350-acre (west)and 185-acre (east) county-owned parcels. This reach is one of the primary chinook salmon spawningareas, and the land purchase will protect this critical spawning habitat.LA GRANGEDAM ❰LAGRANGEWATERFORDRiverHICKMANGRAVEL MINING REACHFLOODWAY RESTORATIONTuolumne River Technical Advisory CommitteeThis 7-mile reach near Waterford (from RobertsFerry Bridge to the Old Reed Rock Plant) supportsactive off-channel gravel mining, and was extensivelydamaged during the 1997 flood. CALFEDand USFWS/AFRP have funded the first of fourphases of this project, with Phase I, the upper twomiles of the project, set to begin in 1999. PhasesII-IV will proceed in subsequent years. Restorationactivities will include increasing floodway capacityto convey at least 15,000 cfs, increasing salmonspawning and rearing habitat, protecting dikesand off-channel pits from future flood damage,and restoring riparian forests on floodplains.SPAWNING GRAVEL SUPPLEMENTATIONCalifornia Department of Fish & Game, TRTACConstruction of La Grange Dam in 1893 permanentlyended gravel supply to downstream reaches of theTuolumne River. Restoring gravel supply to the TuolumneRiver below La Grange Dam will greatly improvesalmon spawning and rearing habitats. The project startswith initial mechanical placement of a large volume ofgravel to begin replacing over 100 years of lost gravelsupply, followed by periodic augmentation to maintainsupply as gravels slowly move downstream during highflows.

13Special Run Pools 9 and 10: A channel reconstruction projectAn excellent way to understand the scope of river restorationon the Tuolumne River is to witness a project in progress. Theopportunity will soon be afforded by the Special Run Pool 9(SRP 9) Restoration Project. SRP 9 is located immediatelydownstream of Fox Grove County Park and is visible lookingwest from the Geer Road Bridge. The Technical AdvisoryCommittee selected SRP 9 as one of the Settlement Agreementprojects, and received approximately $2.5 million in fundingfrom CALFED and USFWS/AFRP. At present, environmentalpermitting and compliance documents are nearing completion,engineers are preparing final design details, and constructionis scheduled to begin in summer of 1999. TheTurlock Irrigation District is administering the project for theTRTAC.SRP 10SRP 9Instream and off-channel gravel mining began in this reach in the 1950s.Today, 30-foot deep pits provide habitat for bass (a predator of juvenilesalmon) and also block sediment movement through this reach.WHAT TO DOSection 12C of the Settlement Agreement specifies “at leasttwo pond isolation projects will be included in the 10 priorityprojects.” The TRTAC considered a variety of alternatives forrestoring SRP 9, such as constructing a dike to separate thechannel from the large backwater pit, or actively removingunwanted predator fish, leaving the pond intact. In the end,the TRTAC determined that the best solution was to refill theentire pit with gravel and cobble to reconstruct a natural riverchannel, restore a natural channel and floodplain form, andre-vegetate floodplains with cottonwoods, valley oaks andother native vegetation. This approach will help restorenatural river processes, provide additional riparian habitat,and improve conditions for chinook salmon by creating newjuvenile habitat and eliminating predator habitat. By trying torestore “ecosystem processes”, in addition to improvingconditions for a single species, the SRP 9 project is essentiallya large-scale experiment, and will be thoroughly monitoredover the next several years to determine if project objectivesare met.As shown in a typical cross section through the SRPs, the existing channelis four times wider and at least two times deeper than it shouldbe. Narrowing the channel will eliminate bass habitat, allow gravelsto move through the reach, and provide floodplains for replantingriparian vegetation.A BRIEF HISTORYBeginning in the 1930s, gravel miners extracted valuable sandand gravel aggregate directly from the river channel, creatinglarge pits in the river with water depths up to 36 ft. Excavatingthese ponds eliminated salmon spawning and rearing habitat,as well as entire floodplains and riparian vegetation. Theselarge pits now trap all coarse sediment (gravel and cobble)carried downstream by high flows, and provide warm-waterhabitat for non-native bass species that eat chinook salmonsmolts as they migrate out to sea. Studies found largemouthbass densities to be as high as 750 adult bass per river-mile.Since every chinook salmon juvenile produced on the TuolumneRiver must pass through this reach, bass have thepotential to consume many thousands of juvenile salmonduring the outmigration season. Reducing bass predation byeliminating their habitat is thus a high priority objective forrestoring the chinook salmon population.When complete, the restored project reach may provide apermanant solution to decades-old problems, and represent asignificant piece of the 52-mile Tuolumne River corridorrestoration effort.In 1937, prior to aggregate extraction, this reach of the Tuolumne Riverhad a natural channel form and floodplain. Riparian vegetation wasscattered across the floodway and gravel bars were exposed at low flows.chinook salmon

G rayson River Ranch: A perpetual conservation easementThe Grayson River Ranch project is an excellent example ofways in which voluntary public participation and leadershipfrom local agencies can make the vision for a Tuolumne Riverfloodway come to life. Located between river miles 5 and 6from the mouth of the Tuolumne River, the 140 acre GraysonRiver Ranch parcel was historically a river floodplain vegetatedwith riparian hardwood species. The property was clearedfor cultivation as early as 1937, and has flooded repeatedlyover the years.14Following the 1997 flood , the property owner applied for andmay receive a Perpetual Conservation Easement for parts ofthe Grayson River Ranch parcel. The USDA Natural ResourcesConservation Service administers easement agreements incooperation with the East Stanislaus County Resource ConservationDistrict, linking with various local, state, federal, andnon-profit (e.g. FOTT) partners. The easement would allow forseasonal flooding and restoration of riparian habitats, whilekeeping the property in the hands of private owners. If theeasement agreement is finalized, the NRCS will develop plansfor restoring the parcel to more natural conditions, whichmay include revegetation with native riparian hardwoodspecies, and/or creating off-channel wetlands. With restoration,this land will provide increased fishery, wildlife, andflood management benefits.A few large stands of riparian vegetation persist along the Tuolumne.Although it took only decades to clear much of the land, centuries oldvalley oaks are not as quickly replaced. This multi-story, diverse canopyarchitecture provides habitat for many species of birds and wildlife.Even with dikes, many parcels of land near the confluence with the SanJoaquin River are frequently flooded (note traces of soil erosion from1997 floods). These former floodplains contain soils of marginal qualityfor agricultural production, and generally support feed crops for livestock.However, they are ideally suited to sustain native hardwood forestsas well as a lush understory of flood-dependent plant species.VALLEY OAKThe majestic valley oak, once a symbolof the native California landscape anda dominant figure in riparian forests,is now nearly gone. Confined to lessthan 2 % of its original habitat state-wide,this flood-dependent native is endemic - it growsnowhere else but in California. Land acquisitions orconservation easements may be the only way to preservethe rare remaining groves of valley oak and allow newtrees to propagate.Before the land along the Tuolumne had been converted to agriculture,old-growth oak forests extended across the floodplain to merge with theforests along the Stanislaus, Merced and San Joaquin Rivers. In 1937,clearing of the Grayson River Ranch parcel was well underway.

Front cover photographs (clockwise from top-left)• Adult chinook salmon returning to the river to spawn• A dynamic gravel bar near Basso Bridge at river mile 49.2• La Grange Dam at river mile 52.2• Mature valley oak and Fremont cottonwood riparian forest“The practice of conservation must spring from a convictionof what is ethically and aesthetically right, as well as what iseconomically expedient. A thing is right only when it tends topreserve the integrity, stability, and beauty of the community,and the community includes the soil, waters, fauna, and flora,as well as the people.”Aldo Leopold, 1947THIS DOCUMENT IS A SUMMARY OF THEHabitat Restoration Plan for the Lower Tuolumne River CorridorPREPARED FORThe Tuolumne River Technical Advisory CommitteeTurlock Irrigation District333 East Canal DriveTurlock, CA 95381(209) 883-8316WITH ASSISTANCE FROMUS Fish and Wildlife ServiceAnadromous Fish Restoration ProgramPREPARED BYMcBain & TrushP.O. Box 663Arcata, CA 95518(707) 826-7794FOR MORE INFORMATION CONTACTORModesto Irrigation District1231 Eleventh StreetModesto, CA 95354(209) 526-7459Printed with soy ink on recycled paperPrinted on a Heidelberg Direct Image, Chemical-Free Press