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Vernalis Adaptive Management Plan (VAMP)
2001 Salmon Smolt Survival Investigation Study Plan

February 13, 2023


The Vernalis Adaptive Management Plan (VAMP) has been developed to provide (1) protection for juvenile Chinook salmon emigrating from the San Joaquin River through the Sacramento – San Joaquin Delta, and (2) an experimental determination of juvenile Chinook salmon survival in response to San Joaquin River flow and State Water Project (SWP) and Central Valley Project (CVP) exports. San Joaquin River flows and SWP/CVP exports are commonly believed to affect survival of juvenile fall-run Chinook salmon emigrating from the San Joaquin River basin. The VAMP experimental investigation and sampling program has been designed to:

  • Serve as the implementation program for the State Water Resources Control Board (SWRCB) 1995 Water Quality Control Plan providing fisheries protection for the lower San Joaquin River;

  • Implement elements of the Central Valley Project Improvement Act (CVPIA) Anadromous Fish Restoration Program (AFRP) Delta actions for the lower San Joaquin River;hatch_ro.jpg (22212 bytes)

  • Implement interim salmon protective measures within a carefully designed experimental structure which will satisfy the need for immediate protection;

  • Provide the scientific information to reduce biological uncertainty regarding the effects of San Joaquin River flow, and SWP/CVP export upon salmon smolt emigration success; and

  • Permit greater efficiency and confidence in future decisions regarding conservation of San Joaquin River Chinook salmon stocks.

The VAMP program employs an adaptive management strategy to use current knowledge of hydrology and environmental conditions to protect Chinook salmon smolt passage, while gathering information to allow more efficient protection in the future.

Vamp Experimental Design Framework

Experimental mark-recapture studies have been conducted in previous years by the California Department of Fish and Game (DFG), and U.S. Fish and Wildlife Service (FWS) that provide valuable insights into factors affecting juvenile Chinook salmon survival. Results of these studies have shown that survival rates for emigrating juvenile Chinook salmon have been low in many recent years. These low survival rates are generally mirrored by low rates of adult escapement 2-1/2 years later, so that improving survival through the Delta is believed, by many, to be an essential part of restoring San Joaquin River salmon runs. Aside from flow and export rate manipulations, installation of a barrier at the Head of Old River has been identified as a key element to improving the survival of downstream migrating salmon. Such a barrier is apt to alter the impacts of flow and export rates on salmon smolt passage and survival.

The experimental design includes both multiple release locations (at Durham Ferry and Jersey Point), and multiple recapture locations (Antioch and Chipps Island; Figure 1) and in the ocean fisheries. The use of data from multiple recapture locations and multiple replicated release series provides a stronger basis for evaluating juvenile Chinook salmon smolt survival as part of the VAMP testing program, than reliance on recapture data from only one sampling location and only one series of releases per year. The VAMP release and recapture locations will be consistent from one year to the next, providing a greater opportunity to assess salmon smolt survival over a range of Vernalis flows, SWP/CVP exports, with the presence of the Head of Old River Barrier. The releases at Jersey Point serve as controls for recaptures at Antioch and Chipps Island, thereby allowing the calculation of survival indices based on the ratio of marked salmon recaptured from upstream and downstream (control) release locations. The use of ratio estimates as part of the VAMP study design substantially reduces the bias associated with differential gear collection efficiency within and among years, and substantially strengthens the analytical ability of the experimental design to detect differences in salmon smolt survival as a function of Vernalis flows and SWP/CVP exports.

The VAMP experimental design measures salmon smolt survival rates under six different combinations of flow and export rates. The experimental design includes two mark-recapture studies performed each year during the outmigration period to provide two estimates of salmon survival under each set of conditions. Each of the mark-recapture studies (two per year) uses tagged San Joaquin River origin juvenile Chinook salmon. Chinook salmon survival rates under each of the experimental conditions are then calculated. Recapture of marked salmon in these investigations is important for improving the confidence in survival rate estimates. The primary recapture locations are Chipps Island, as in previous studies conducted by the FWS, and at an intensively sampled location in the lower San Joaquin River near Antioch, at the SWP and CVP fish salvage facilities, and in the ocean fishery.

VAMP 2001 Study Plan

The VAMP 2001 Study Plan was developed using the framework established for San Joaquin River Chinook salmon smolt survival investigations. Refinements of the VAMP study plan will be coordinated through the San Joaquin River Technical Committee Biology and Hydrology groups.

Location ot VAMP 2001 proposed release sites (Durham Ferry and Jersey Point), recovery locations (Antioch and Chipps Island, and Upper Old River barrier location within the Sacramento-SanJoaquin RiverDelta/Estuary.

Figure 1: 

Location ot VAMP 2001 proposed release sites (Durham Ferry and Jersey Point), recovery locations (Antioch and Chipps Island, and Upper Old River barrier location within the Sacramento-SanJoaquin RiverDelta/Estuary.

 Anticipated Operating and Environmental Conditions

Preliminary forecasts of San Joaquin River Basin runoff, reservoir storage, and San Joaquin River flow levels will be used by the hydrology technical team to identify VAMP 2001 operational alternatives. Coordination with San Joaquin River tributary investigations has been initiated. During the 2000 spring pulse flow the temporary barrier at the Head of Old River was almost overtopped and review of the situation concludes that a target of 7000 cfs at Vernalis could not be safely passed with a present design of the temporary barrier in place. Various alternatives are being evaluated. A new operational plan is being proposed for the south Delta barriers (Head and three agricultural barriers) and the permitting process is underway. Additional refinements to the San Joaquin River flow levels, SWP and CVP exports, and Old River Barrier operations will continue through the spring as new information on anticipated operations and hydrologic information becomes available. The final VAMP 2001 experimental test conditions are anticipated to be established by early April.

Coded-Wire Tagged Salmon Allocation and Release Strategy

The San Joaquin River Group Authority submitted a request on January 22, 2001, to the California Department of Fish and Game for up to 400,000 juvenile Chinook salmon to release as part of VAMP 2001 studies. Releases would be made twice in approximately mid-April and late-April, 2001. The various study plans depending upon the number of Merced River Hatchery juvenile Chinook salmon made available for 2001 VAMP survival studies is summarized below:

Mid-April Late April
If 250,000 fish were available:
Durham Ferry 75,000 75,000
Jersey Point 50,000 50,000
TOTAL 250,000
If 300,000 fish were available:
Durham Ferry 75,000 75,000
Mossdale 50,000
Jersey Point 50,000 50,000
If 350,000 fish were available:
Durham Ferry 75,000 75,000
Jersey Point 50,000 50,000
If 400,000 fish were available:
Durham Ferry 100,000 100,000
Mossdale 50,000 50,000
Jersey Point 50,000 50,000
Further evaluation of the 2000 data will be made and may change the anticipated study design. Pending that analyses, these study plans are those that would be used in 2001. 

Coded-Wire Tagging

Each of the VAMP 2001 releases of coded wire tagged salmon would be comprised of multiple tag codes of approximately 25,000 fish each. For example, the release of 75,000 coded wire tagged salmon at Durham Ferry would be comprised of three separate tag codes of 25,000 fish each which would be released during each test to provide the opportunity for estimating variance in survival indices within each release group. The biology group is presently evaluating the benefits of higher release numbers per group instead of keeping tag codes separate at the hatchery. A choice, between the two options, is necessary because of the limited space for holding separate groups at the hatchery.

Prior to and after coded-wire tagging, juvenile salmon will be inspected for evidence of disease and parasites. Fish health inspections will be performed by a fish pathologist. Any group of marked fish showing unusually high mortality within the hatchery holding facility prior to or after marking, or evidence of disease or other pathogens which cannot be effectively treated, will not be released as part of these tests. Additional observations of fish health conditions after release will be made for a sub-sample of marked fish held in live cars at release locations (see discussion below).

The VAMP 2001 coded-wire tagging will be subject to a quality control/quality assurance program to ensure that juvenile salmon have been effectively tagged, and to document tag retention. The quality control/quality assurance program includes a standard magnetic detector to separate tagged and untagged salmon as they are released from the tagging machine. A second quality control check occurs prior to release of the marked fish. A sub-sample of marked fish from the hatchery holding facility will be processed using a tag detector to document coded-wire tag retention and tags will be processed to verify appropriate tag codes for each release group. Tag codes will be verified for a sub-sample of 50 fish per 25,000 marks. The sub-sample of fish from the hatchery holding facility will also be examined to quantify the percentage of marked fish having a recognizable adipose fin clip. The total number of each coded-wire tag group released will be calculated based on the actual number of fish marked (actual count) adjusted to account for post-marking mortality within the hatchery holding facilities, a correction factor for coded-wire tag retention, a correction factor for adipose fin clipping, and an adjustment for mortality occurring during loading and transport of marked fish to the release site. Data on length and weight for a sub-sample of each marked group (approximately 200 fish) will be made to document both the length-frequency distribution, and length - weight relationship (condition factor) for each test group. These fish will be held in live cars as part of the quality control program for each release group (see discussion below).

Tag codes will be coordinated with other salmon evaluation programs and with the statewide tag coordinator. All juvenile Chinook salmon, which are coded-wire tagged, will also receive an adipose fin clip.

Tagged Fish Transport

hatch_truck.jpg (20680 bytes)Juvenile salmon will be transported from the Merced River Fish Hatchery to the release location in water of comparable temperature to that occurring within the hatchery. Water temperature will be monitored within the hatchery rearing facilities, transport truck, and release site, to identify and document any potential thermal stress occurring as part of the fish release.

Coded-wire tagged salmon will be released, when possible, at an average length of 75 mm or greater. To the extent possible, releases at Jersey Point will be made on a flood tide.

Live Car Holding

As part of the VAMP 2001 mark-recapture studies, juvenile Chinook salmon will be held in situ in live cars in the vicinity of each of the release locations. Live cars are constructed of a PVC frame and non-toxic screen mesh. A sub-sample of juvenile Chinook salmon will be removed from the transport truck for holding in the live cars. Observations right after release and after the 48 hour holding period include mortality, condition of the eyes, general body and gill color, determination of whether any fin hemorrhaging was evident, percent scale loss and overall vigor. These observations are intended to identify the occurrence of poor condition and/or major mortality in a release group, which may result from factors such as handling stress during transport and release, that would influence the validity and interpretation of the corresponding group of marked salmon released into the river as part of VAMP 2001 survival studies.

After 24 hours, an additional sub-sample of the fish held in the live cars will be sampled for disease and physiological condition by the U.S. Fish and Wildlife Fish Health Center. Hematocrit and leukocrit measurements will be conducted on blood samples and kidney and internal organs will be examined for parasites and bacterial and viral pathogens. ATPase levels will also be measured from gill tissue.

At the completion of the holding period all marked fish held in the live cars will be sacrificed, and the carcasses will be temporarily archived as part of the QC program to ensure the integrity of each mark group. A sub-sample of 25 tags will be processed to verify tag codes for each release group. Additional tags would be processed if tag code errors are identified. Based on results of this QC check a decision will be made regarding the validity of the release for inclusion in subsequent analyses.

Recapture Methods and Locations

Fishery Sampling - View fish sampling reports

Sampling at Chipps Island using a midwater trawl will be performed by the U.S. Fish and Wildlife Service. Sampling effort at Chipps Island has been typically 10, 20-minute tows during morning hours each day. Additional sampling at Chipps Island has been added during the VAMP period to augment the recovery of the marked fish as part of the VAMP experiment. This additional sampling includes a second shift of 10, 20-minute tows during the afternoon-evening hours each day.

Fisheries sampling as part of VAMP 2001 will be conducted in the vicinity of Antioch on the lower San Joaquin River using a Kodiak trawl. A Kodiak trawl has a graded stretch mesh, from 2-inch mesh at the mouth to ?-inch mesh at the cod-end. Its overall length is 65 feet, and the mouth opening is six feet deep and 25 feet wide. A General Oceanics flow meter will be used to estimate the volume of water sampled during each collection, for use in calculating catch-per-unit-of-effort (CPUE). The net is towed between two skiffs. Trawl duration is approximately 20 minutes, sampling in an upstream direction. Approximately 36 samples are collected each day. Trawls in the lower San Joaquin River at Antioch are performed parallel to the left bank, mid-channel, and right bank to sample coded-wire tagged salmon emigrating from the San Joaquin River.

Recovery of coded-wire tagged salmon at the State and Federal Water Project salvage operations will be conducted as part of routine monitoring.

Ocean adult recoveries will also be evaluated as part of this fishery resource investigation.

A preliminary effort at Benicia may occur in 2001 to evaluate whether absolute survival between Mossdale/ Durham Ferry and Jersey Point is similar using recaptures at Benicia. Some funding has been allocated for the project, but additional funding is necessary before the sampling can be conducted.

Seasonal Timing

Fishery sampling as a direct element of the VAMP 2001 survival studies will be conducted from April 15 to May 15. Sampling will continue as part of this investigation (potentially at a lower level of intensity) from May 16 to June 1 to evaluate the ramping period and to continue to collect marked fish emigrating from the system. Exact dates of sampling will be determined in response to any changes in the dates of fish release.

Sample Processing

Juvenile Chinook salmon having an adipose fin clip, indicating the presence of a coded-wire tag will be sacrificed, placed in individual, labeled, plastic bags and held on ice until they can be frozen. The frozen samples will be provided to the U.S. Fish and Wildlife Service office in Stockton for coded-wire tag removal and processing.

Delta smelt, splittail, and other fish (excluding adipose marked juvenile Chinook salmon) collected will be enumerated, measured and released at a location downstream of the sampling site immediately after enumeration and measurement. No fish will be transported more than ? mile from the sampling site. Field personnel note and keep any listed fish that have not survived the process for proper disposal.

Incidental Take Permits

Incidental take authorization for fish species listed for protection under the California and Federal Endangered Species Acts for the Chipps Island sampling is covered by Interagency Ecological Program (IEP) and U.S. Fish and Wildlife Service permits.

The U.S. Bureau of Reclamation is in Section 7 consultation with the National Marine Fisheries Service for incidental take authorization of chinook salmon and steelhead for the Antioch sampling. Incidental take authorization for Antioch sampling for delta smelt and splittail is being developed through a Section 7 consultation between the U.S. Bureau of Reclamation and U.S. Fish and Wildlife Service. The California Department of Fish and Game issued a Memorandum of Understanding (MOU) (Section 2081(a)) authorizing the take of species protected under the California Endangered Species Act for sampling at Antioch.

Operational and Hydrologic Monitoring

USGS, USBR, and DWR will perform hydrologic monitoring within the lower San Joaquin River and Delta during the VAMP 2001 survival tests. Information on water surface elevation and flow measurements at established monitoring locations throughout the lower San Joaquin River and Delta will be used to document conditions during each test period.

Detailed operational records of SWP and CVP operations (e.g., Clifton Court gate operations, hourly export rate and volume) will be maintained to document operational conditions during the VAMP 2001 test.

Water Quality Monitoring

Routine water quality monitoring will be performed from April 1 through June 1 each year. Water quality monitoring will include, but not be limited to, water temperature, and electrical conductivity. Water quality monitoring performed specifically as part of the VAMP 2001 test will complement routine baseline water quality monitoring performed by the Department of Water Resources.

Water temperature will be monitored using individual computerized temperature recorders (e.g., Onset Stowaway Temperature Monitoring/Data Loggers). Ten temperature monitoring locations (Figure 2) will include fish release sites within the San Joaquin River (Durham Ferry and Jersey Point), and locations along the San Joaquin River and interior Delta channels used as migratory pathways for juvenile Chinook salmon released as part of these tests.

Water temperature will be recorded at approximately 20-minute intervals throughout the period of the investigations. Temperature recorders will be located near the surface and near the bottom at selected stations to determine potential vertical stratification in temperature.

Proposed water temperature monitoring locations for the VAMP 2001 study.

Figure 2: 

Proposed water temperature monitoring locations for the VAMP 2001 study.

Analysis and Interpretation of Results

Biological and physical data to be recorded as part of VAMP 2001 will then be critically reviewed to ensure that the smolt survival data are appropriate for subsequent use in statistical analyses. Data from each test will be available to all interested parties for independent review and analysis.

Absolute survival between Durham Ferry and Jersey Point will be plotted against flow and exports. The table of target flows and export rates will also be evaluated at the conclusion of each year to determine which combination of targets is desired for following years.

After several years of conducting the VAMP survival investigations mark-recapture data will be analyzed in a way similar to that done on the Sacramento River (Newman and Rice, 1998), where the log of the recoveries would be modeled using a linear combination of covariates. The model would be fitted using weighted least squares as was done for the Sacramento River data. Replicates within a year will increase the estimated precision of coefficients and strength of the analyses. Recovery data from the ocean fishery will add precision. All the data will be used simultaneously to estimate the model parameters and to determine the respective associations of flows and exports on salmon smolt survival. Attempts also will be made to describe the associations between San Joaquin River flow and export to smolt survival.

VAMP Documentation Reports

Results of coded-wire tag processing, documenting the numbers of juvenile salmon from each tag group released, in association with data on the operating and environmental conditions occurring during the VAMP 2001 study, will be documented and made available as part of the annual technical report.

The following is a preliminary budget for the expenses associated with VAMP Monitoring Program in 2001.



Tagging- Supervision and Labor $45,000
Tagging-Supplies 28,000
Rearing of VAMP fish at MRFF (Biologist and Tech.) 26,000
Landing Mat for Fish Trailer 1,000
Small Trailer for fish transport 5,000
Feasibility study for increasing fish production at MRFF 10,000
Transport and release of test fish (tractor rental) 4,000
Antioch Sampling 190,000
Report by Hanson Environmental 25,000
USFWS –in kind services
Partial funds for trawling at Benicia during VAMP 12,000
Second shift sampling at Chipps Island: 30,000
Coded wire tag processing: 15,000
Data entry/data management: 5,000
Net pen studies: 5,000
Analysis, report writing, and meeting attendance: 15,000
Physiological studies: 9,000
Total cost of USFWS in-kind services 91,000

Total cost of 2001 Program



Dennis W. Westcot, Project Administrator
San Joaquin River Group
716 Valencia Ave.
Davis, CA 95616-0153
(530) 758-8633
[email protected]

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