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PROGRAM ACTIVITIES OF THE INTERAGENCY ECOLOGICAL PROGRAM FOR THE SACRAMENTO-SAN JOAQUIN ESTUARY
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MAY 1, 1995

Entrapment Zone Studies

Contact Person: Wim Kimmerer (SFSU) (510) 525-9073

In 1994 the IEP conducted its first comprehensive, multidisciplinary field study of the relationship between the physical and biotic components of the environment in the Estuary's entrapment zone. A similar effort is planned for the early summer of 1995 under high flow conditions, which will provide a useful comparison with 1994' results, which were obtained under very low flow conditions. The purpose of the study is to determine how organisms and particles are maintained in this biologically productive zone, particularly in regard to the roles that freshwater flow, and vertical and horizontal salinity gradients play. This study is a multi agency/university investigator effort conducted under the auspices of the program's Estuarine Ecology Team. The major components of the 1995 study are:

Three 30-hour synoptic sampling cruises involving the near continuous collection of phytoplankton, zooplankton, and larval fish from throughout the water column via pump sampler. Continuous bottom to surface current profiles will also be measured continuously using boat mounted acoustic Doppler current profilers. Collections will be made from three boats "sitting" continuously on the 1, 3, and 6 mS/cm bottom isohalines, respectively.

Continuous multi-month measurement of currents, conductivity, temperature, depth, and optical backscatter at a total 11 sites in the main channel and adjacent embayments roughly between Benicia and Chipps Island. Continuous meteorological data (wind, atmospheric pressure, etc.) will be obtained from Chipps Island. This is the most intensive, detailed effort ever attempted in the Estuary to measure and interpret hydrodynamic related conditions.

Trophic Relationships

Contact Person: Wim Kimmerer (SFSU) (510) 525-9073

The IEP's Estuarine Ecology Team, made up of university, consulting, and agency scientists is working on a number of projects designed to improve the understanding of (and the availability of information about) the Estuary's trophic relationships. These projects include:

A study by Dr. Peggy Lehman of DWR of the long term changes in the biomass and distribution of Melosira granulata in the upper estuary, including the contribution it makes to carbon loading within Suisun Bay and the southern Delta.

A investigation by Dr. Tim Hollibaugh (SFSU) of the role that micro zooplankton plays in the trophic dynamics of the estuarine food chain prompted by the discovery of high bacterial production in the upper estuary based on-river-inflow derived organic matter.

Assembling the current state of the knowledge of the lower trophic levels of the Estuary into a single document for the purpose of developing conceptual models and identifying appropriate research topics from.

A specific water Agreement prompted effort to identify, categorize, and report potential species by species and overall ecosystem X-2 related controlling mechanisms to facilitate research planning efforts associated with the Agreement.

D. ESTUARINE MONITORING

Contact person for Fall Midwater Trawl Survey, Striped Bass Egg & Larvae Survey Data Analysis, and Neomysis/Zooplankton Study. Contact Person: Mr. Lee Miller (DFG), (209) 948-7800

The IEP includes several routine monitoring elements providing long-term measures of fish and invertebrate species abundance and distribution and water quality. The Fall Midwater Trawl Survey, for example, provides a nearly continuous record of the abundance and distribution of the juvenile fishes in the upper estuary since 1967. Information from these long term survey elements has played a very large role in Estuary management and protection because little other information was available. However, most recently the IEP has conducted more of special studies, especially related to special status species. Nevertheless, data from the long term surveys are valuable for tracking resource trends in the Estuary. The Summer Townet Survey and the Fall Midwater Trawl Survey have become important components of ESA monitoring for delta smelt although originally their purpose was to measure long-term striped bass abundance.

Fish Monitoring

Summer Townet Survey:

Contact Person: Lee Miller (DFG) (209) 948-7800 Since 1959, this survey has indexed the abundance of young striped bass when the average size is 38 mm by sampling 31 stations from San Pablo Bay through the Delta. The original purpose was to predict recruitment to the adult stock but the index has proven valuable in gauging the environmental health of the estuary. Young striped bass abundance is primarily a function of Delta outflow, Delta water exports and egg production. Abundance indices for other species have also revealed important trends. For example, the index for delta smelt was useful in determining its status as a threatened species. This survey is mandated by the 1995 USFWS Biological Opinion (BO) for delta smelt on the operation of the SWP and CVP.

Midwater Trawl Survey:

Contact Person: Lee W. Miller, CDFG (209) 942-6107

Since 1967, midwater trawl surveys have been conducted monthly from September-December to index the abundance of young- of -the-year and other age groups of fishes. Relationships between abundance and environmental conditions have been developed for several species. Since 1992 the survey has added sampling from January to April for measurement of the distribution of delta smelt for defining the timing of their spawning migration. Because of the Framework Agreement and the new standards in the spring it is appropriate to monitor fish trends through the period May-August as well. The EMPWT will evaluate augmenting this survey.

The fall mid water trawl sampling was used in the 1994 USFWS BO to determine the ôtake limitö at the SWP and CVP. It is also mandated in the 1995 BO for delta smelt and the Delta Native Fishes Recovery Plan to monitor status of delta smelt.

San Francisco Bay Monitoring:

Contact Person: Chuck Armor (DFG) (209) 948-7800

Otter and midwater trawls have been used since 1980 to track the abundance and distribution of marine and estuarine fish, shrimp and crabs at 52 channel and shoal stations from South San Francisco Bay to the Lower Sacramento and San Joaquin rivers. Numerical and size frequency data are collected on all fishes, shrimp and Cancer crabs. Additional sampling is done with baited ring-nets at 12 stations for dungeness crabs. Relationships between abundance of several species and environmental conditions have been described. Recently, we reduced the midwater trawl to monthly surveys downstream of Carquinez Strait from April to December. The midwater trawl survey described in the previous section will measure abundance trends of estuarine species of interest in Suisun Bay and the Delta. The data base is longer and the geographical coverage upstream is greater for this survey.

Adult Striped Population Study:

Contact Person: David Kohlhorst, DFG (209) 948-7800

Since 1969, Petersen population estimates by age class and sex have been made using tag and recapture methods. Striped bass are tagged every other year on the San Joaquin River and Sacramento River and released on the their spring spawning migrations. Tagged fish are measured, sexed and aged. A creel census is conducted in the summer and fall to ascertain tagged to untagged ratios and to determine the size and age composition of the catch. Mailed tag returns (corrected for non-response using reward tags) are used to estimate annual harvest rates, mortality rates and migrations of striped bass. Striped bass adults have declined in numbers and average size over the study period.

Sturgeon Study:

Contact Person: David Kohlhorst, DFG (209) 948-7080

Life history aspects of white and green sturgeon are studied to develop management strategies to maintain the populations. Adult abundance and harvest rates and natural mortality measurements are made in two year consecutive efforts about three years apart using tag and recovery methods. Other studies include aging the population, determining spawning areas, spawning migrations and juvenile distribution and abundance.

Resident Fish Survey:

Contact Person:
        Randall D. Baxter
        Associate Biologist (Fisheries/Marine)
        California Dept. of Fish and Game
        Central Valley - Bay Delta Branch
        4001 N. Wilson Way
        Stockton, California  95205
        (209) 942-6081
        rbaxter@delta.dfg.ca.gov

Contact Person (old): David Kohlhorst, DFG (209) 948-7080

This program is a renewal of sampling done in the 1980s to measure abundance trends of resident shoreline fishes in the Delta. Twenty selected sites are sampled by electrofishing every other year beginning in spring 1995. Sampling is conducted every other month from February to August.

Invertebrate Monitoring

Neomysis and Zooplankton Survey: Contact Person: James Orsi, DFG (209) 942-6087 through Relay 800-735-2922

This survey, conducted since 1971, monitors the concentration of Neomysis sp and zooplankton at 35 core stations in the Suisun Bay and the Delta. Surveys are conducted twice per month from March to November. Sampling effort in 1995 was reduced to 16 stations and integrated with the discrete water quality monitoring (see below). Concentrations per cubic meter of zooplankton and Neomysis (by mm size group) are determined.

Water Quality, D-1485 Compliance Monitoring

The SWRCB Water Quality Control Plan D-1485 monitoring has been consolidated to provide continued long-term surveillance and streamlined to permit resources to be used for additional studies and real time, compliance monitoring capabilities. The water quality program has submitted plans to the SWRCB for expanding the continuously recording, multi parameter network. The telemetry capabilities are being enhanced so that critical parameters which could affect operations can be monitored in real time.

Discrete Water Quality Sampling: Contact Person: Leo Winternitz, DWR (916) 227-7548

Water quality samples are collected by boat monthly or semi-monthly at 26 sites in San Pablo, Suisun Bay and the Delta for determining impacts of the State and Federal Water Projects on the environment and to determine compliance with water quality standards established by State Water Resources Control Board (as prescribed in Table III of D-1485). Monitoring also includes a phytoplankton element, which measures species composition and abundance at 18 sites, and a benthos sampling element, which measures composition and abundance at 5 locations. Sampling for all elements, except benthos, has been conducted since 1971. Benthos monitoring was initiated in 1975 and sampling is currently monthly with occasional extended sampling of the entire estuary to measure the distributional changes of exotic species such as the Asian clam, Potamocorbula amurensis, to evaluate their possible effects on the estuarine food web.

Continuous Water Quality Monitoring:

Contact Person: Leo Winternitz, DWR (916) 227-7548

The research vessel San Carlos is equipped with sensors that permit continuous display and recording of water quality parameters. These can detect water quality anomalies needing further investigation. Additionally, 6 stationary, on shore, recorders and sensors measure and record dissolved oxygen, pH, specific conductance, air and water temperature, wind velocity and direction, solar radiation, tide stage and in-vivo chlorophyll. These data can be accessed by telemetry from Sacramento. This system will be further improved and upgraded so that new SWRCB Water Quality Control Plan compliance can be accomplished by real time monitoring.

San Joaquin River Dissolved Oxygen Monitoring: Contact Person: Leo Winternitz, DWR (916) 227-7548

Dissolved oxygen is monitored at sites in the Stockton Ship Channel near Stockton during the late summer and early fall of each year because levels can drop below 5.0 mg/L due to low flow, high water temperatures and high biochemical oxygen demand (BOD). Low dissolved oxygen levels are deleterious to migrating adult salmon and other aquatic life. Monitoring is usually done in conjunction with the placement of a rock barrier at the head of Old River to improve net downstream flows for migrating chinook salmon. This program was initiated in 1969.

E. FISH FACILITIES DEVELOPMENT

Contact Person: Mr. Darryl Hayes, DWR (916) 227-7546

The term fish facilities is used here to describe fish screens and guidance structures, and other protective facilities designed to reduce impacts on fishes. Fish facilities development has always been a major component of the IEP and has generally been closely tied to Delta water project planning. For example, in the late 1970's and early 1980's there was a major IEP effort to develop fish screening and return facilities for the Peripheral Canal intake. The following are the present fish facility activities of the program.

Delta Smelt Screen Criteria Development

Historically, fish screen criteria research in the Delta has focused on recreationally and commercially important species such as chinook salmon and striped bass. At the time of the ESA listing of delta smelt, essentially no screen criteria information was available for this species. Recent USFWS biological opinion established conservative screen criteria for delta in lieu of firm information. The IEP, through support of U.C. Davis researchers, is evaluating swimming abilities of delta smelt relevant to current screen criteria of 0.33 fps and 0.20 fps. Research includes developing information on environmental tolerance limits of salinity and temperature for all life stages of delta smelt, evaluations of critical and endurance swimming performance, and morphological measurements for different life stages. Proposed research will also study behavioral aspects of swimming abilities at screened diversions. The goal is to develop relevant screen criteria for delta smelt protection.

Georgiana Slough Acoustic Fish Barrier

Contact Person: Darryl Hayes, DWR (916) 227-7546

Past IEP research on the juvenile salmon survival in the Delta indicates that emigrating smolts entering the central delta through the Delta Cross Channel and Georgiana Slough survive at lower rates than those remaining in the Sacramento River. Since 1993, the IEP has been working in cooperation with the San Luis & Delta-Mendota Water Authority to test the efficacy of using an acoustic barrier at the head of Georgiana Slough (on the Sacramento River, near Walnut Grove) to guide emigrating smolts away from entrance to the Slough. In 1995 the IEP is continuing to evaluate the effectiveness of the barrier and assess the potential for any unintended negative impacts of barrier operations. Major elements of the 1995 evaluation include:

Continuation of the guidance studies using hydroacoustics and trawl sampling for emigrating and experimentally released smolts under the high flow conditions anticipated for the spring of 1995. Note: Extremely high flows in the spring of 1995 prevented placement of the barrier.

Continuation of acoustic signal exposure testing on delta smelt and splittail.

Investigation of the effects of barrier operation on the upstream migrations of of adult salmon and striped bass

In addition, the trawl sampling work will be part of the pilot real time monitoring of fisheries in the Bay-Delta conducted for May and June of 1995.

North Delta Demonstration Fish Protective Facilities Program

Any new diversion on the Sacramento River near Hood, whether to supply an isolated conveyance facility or a new connection to the Mokelumne River, will have to be screened to protect fishery resources. The purpose of this program is two fold: 1) to determine a feasible means of screening fish at this location over a range of possible diversion rates and operational conditions, and; 2) evaluate proposed and existing fish facilities and/or participate in research studies (i.e. G.C.I.D., Red Bluff Research Pumping Plant, etc.) to help design fish facilities that relate to improvements and further development of other major SWP and CVP projects (including CCWD's Rock Slough pumping plant).

Fish Screen Criteria Development - Two-Vector Velocity Flows

(Fish Treadmill)

The purpose of this element is to determine how Delta fish species of various sizes and swimming abilities might behave if subjected to a physical screened barrier at a water diversion. These tests are part of a larger program designed to resolve some of the technical, biological, and environmental issues related to screening diversions from the Sacramento River, although benefits to developing better screen criteria for other facilities should be achieved. The Principles Agreement associated with the December 15, 1994 water accord has outlined a major fish screening component for implementation. This program will help identify adequate designs.

Bacon Island Fish Screen Test

Contact Person: Katie Wadsworth, DWR (916) 227-0180

In association with the Delta Agricultural Diversion Evaluation (see Section II. F. below) tests are being conducted at a Bacon Island agricultural diversion to determine the effectiveness and reliability of a Lakos-Plum Creek type self cleaning fish screen. Testing is conducted April through September. Evaluations are being conducted for all life stages of Delta fish species encountered at the site. Temperature, specific conductance, and diversion rate are monitored.

F. DELTA AGRICULTURAL/MUNICIPAL DIVERSION EVALUATION

Contact person for Southern Delta Entrainment Monitoring and Delta Agricultural Diversion Evaluation: Ms. Stephani Spaar, DWR (916) 227-7536.

There are about 1800 individual agricultural and municipal water diversions in the Delta. The IEP is conducting several independent monitoring and research efforts that collectively:

  • Provide information on the vulnerability and rates of entrainment fish at these diversions
  • Explore means to reduce entrainment at these smaller (<500 cfs) Delta diversions

Each of the projects is being done for different specific purposes or to meet different "mandates" as described individually below. Several studies began after about 1991 when ESA monitoring requirements began, and included consideration of ESA requirements in the initial study design with and some ESA related modifications made more recently. Some of the older projects have been revised in recent years specifically for ESA purposes, such as an expanded sampling of season, increased sampling intensity, and the addition of specific sampling sites.

Contra Costa Canal Intake Entrainment Study:

Contact Person: Jerry Morinaka, DFG (209) 835-3878 or (209) 948-7800

Juvenile and adult Delta fish species including winter- run Chinook salmon, delta smelt, longfin smelt, and splittail are targeted. A large, single-fyked variable mesh sieve net with wings is used to sample the canal downstream of the first pumping plant. Sampling occurs October through August and varies with intensity throughout this period. A 500 micron mesh plankton net samples for small juvenile smelt and splittail from January through July and varies with intensity throughout the period. Water temperature, conductivity, and turbidity are measured during each sampling effort at the sample site. The purpose of the study is to determine the impacts on Delta fish species resulting from the diversion of Delta waters through the unscreened Rock Slough intake of the Contra Costa Canal, and provide information for the assessment of how, where, and if the intake channel should be screened.

Mallard Slough Monitoring Program:

Contact Person: Jerry Morinaka, DFG (209) 835-3878 or (209) 948-7800

Juvenile and adult Delta fish species with an emphasis on winter-run Chinook salmon and delta smelt are targeted. In the pilot sampling year, 1995, various gear types will be used in the intake channel to determine the most effective gear for juvenile salmon (fyke net, boat deployed seine, modified trawl net). Sampling will occur only when the Mallard Slough Pumping Plant is in operation. Larval and small juvenile fish will be sampled using a 505 micron mesh plankton net towed within the intake channel and outside in the Sacramento River every 8 days, April 15-July 15. The purpose of the study is to monitor the relative abundance of fish species vulnerable to entrainment when Delta waters are being diverted through the unscreened intake of the Mallard Slough Pumping Plant, and to determine if the diversion should be screened, and if so, how.