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PROGRAM ACTIVITIES OF THE INTERAGENCY ECOLOGICAL PROGRAM
FOR THE SACRAMENTO-SAN JOAQUIN ESTUARY
4 of 4
MAY 1, 1995

Southern Delta Entrainment Monitoring:

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

Although this monitoring effort was originally designed to provide estimates of egg and larval striped bass entrainment into the CVP and SWP intakes, the survey also provides information on larval delta smelt, longfin smelt, splittail, and other species of concern are targeted. An oblique tow is made with an egg and larval sled with 505 micron mesh. Sampling occurs early February through mid-July. Surface and bottom specific conductance (SC, uS/cm) and surface temperature (degrees Celsius) are measured using a portable conductivity meter. Water transparency is measured (cm) using a secchi disc. Tide is recorded (high slack, ebb, low slack, or flood). Bottom depth (feet) is also recorded. The purpose of the study is to estimate annual entrainment losses of targeted species to the SWP and CVP intakes in the southern Delta, and determine abundance and distribution of these species in the southern Delta and impacts of SWP/CVP operations and the South Delta Temporary Barriers Project.

North Bay Aqueduct Entrainment Monitoring:

Contact Person: Jenni Lott, DFG (209) 948-7800

Striped bass eggs and larvae and larval delta smelt, longfin smelt, splittail, and other species of concern are targeted. An oblique tow is made with an egg and larval sled with 505 micron mesh. Sampling occurs early February through mid-July. Surface and bottom specific conductance (SC, uS/cm) and surface temperature (degrees Celsius) are measured using a hand- held conductivity meter. Water transparency is measured (cm) using a secchi disc. Tide is recorded (high slack, ebb, low slack, or flood) reading. Bottom depth (feet) is also recorded. The purpose of the study is to estimate annual entrainment losses of targeted species to the NBA intake, and determine abundance and distribution of these species in Barker and Lindsey sloughs, impacts of NBA operations, and presence of delta smelt in Barker Slough.

Diversion Evaluation:

Contact Person: Tracy Woods, DWR (916) 227-0437

This project examines the entrainment of all fish species in Delta agricultural diversions, but emphasizes delta smelt entrainment. A 505 micron mesh egg and larval net anchored instream and 1/8" mesh fyke-type net covering the diversion outfall are used to capture entrained fish. An egg and larval sled, townet, and trawls (otter, midwater) are used in adjacent Delta channels. Sampling is conducted mainly April through October. Specific conductance (SC, uS/cm), water temperature (degrees Fahrenheit), diversion flow (cfs, acre-feet) are measured. In addition, channel sampling also includes water transparency (cm) using secchi disc, tide, and bottom depth. The purpose of the study is to determine the magnitude of and factors affecting losses of fish to Delta agricultural diversions, including the susceptibility of fish species and life stages to diversions relative to their abundance and life stages in adjacent channels.

G. CLIFTON COURT FOREBAY PREDATOR/PREDATION CONTROL

Contact person for Clifton Court Forebay Temperature Study Contact Person: Mr. Terry Tillman (DFG), (209) 948-7800

The SWP's Delta water export facilities, located near the town of Byron, include 2100 acre Clifton Court Forebay. Water enters the forebay from West Canal through a set of tidally operated radial gates located on the southeast corner of the forebay. The John E. Skinner Delta Fish Protective Facilities, where fish entrained by the SWP are screened, is located about 2.5 miles away at the southwest corner of the forebay on the canal leading to the Harvey O. Banks Pumping Plant. Since the mid 1970's investigations have been conducted to assess the extent, causes, and means of reducing losses of entrained fish occurring between the radial gates and the protective facilities. These losses have commonly been referred to as pre-screen losses. Pre-screen fish losses and possible related factors are being investigated for a variety of purposes, including:

- Article VII of the DWR/DFG Pumping Plant Agreement calls for the implementation of a plan to reduce CCF predation losses to entrained fish.

- The impact and mitigation information needs of the SWRCB Bay-Delta hearing process, DWR's Delta Water Management Program development, CVPIA implementation, and water transfer proposals.

- Predator removal and predation evaluation efforts are likely to be required as measures to reduce SWP impacts on winter-run chinook salmon and delta smelt, as per the newly amended NMFS and USFWS CVP/SWP biological opinions.

In addition, the Program of Implementation in the SWRCB's 1994 Draft Water Quality Control Plan contains provisions (2.b.) potentially requiring reductions in the loss of entrained fish at the SWP export facilities in part through predator control. Another major reason for developing a better understanding of the extent of, and factors affecting, pre-screen loss is to improve the overall estimates of SWP entrainment loss, which plays such an important role in management of the Estuary.

The fundamental questions addressed by the current and proposed Clifton Court Forebay include the following:

- To what extent do pre-screen losses in CCF contribute to total SWP export facility losses and what factors influence CCF losses?

- What are the predatory fish dynamics primarily of the striped bass population feeding in the Forebay? (An adequate understanding of predator striped bass population dynamics in CCF will dictate what population/predation control measures are viable.)

- What predatory fish control measures offer tenable solutions to the entrained fish loss dilemma?

The current and proposed elements of the 1995 program include:

Pre-screen Fish Loss

Contact Person: Jennifer Bull, DFG (209) 948-7095

Pre-screen loss studies to estimate losses of juvenile salmon across CCF, using spray-dyed hatchery smolts released at the radial gates and recovered at the salvage facilities. These type studies were suspended in 1994, but will resume in 1995 pending improvements in monitoring juvenile escapement through the radial gates. Experiments planned for December 1995 will include a "wild-fish" (captured emigrating juveniles) release component. The objective is to obtain more accurate pre-screen loss estimates than have been obtained in the past).

Fisheries-acoustics monitoring at CCF radial gates and the outlet channel. The objective of this work is to acoustically measure the relationship between fish entrainment at the forebay radial gates and fish salvage at the Skinner Fish Facility repeatedly under various conditions, in order to construct a predictive model for entrainment loss across the forebay.

Water project operations monitoring to comprehensively investigate the effects of various operations sequences/combinations on fish entrainment and pre-screen losses in CCF, including timing of export pumping and radial gate operations, relative operations at the State and Federal projects, and the water route taken to the pumps (for example Italian Slough or Clifton Court Forebay). The immediate objectives are to identify operations that can be modified, and to rank operating scenarios in descending order of cost or difficulty to modify. Secondary objectives are to develop evaluation criteria for managers in assessing and considering options and alternatives for pre-screen loss reduction under various conditions. The goal is to develop operations scenarios that minimize pre-screen losses under ambient environmental conditions; seasonal fish migration, water temperatures, delta flows, etc.

Predator Dynamics

Contact Person: Bob Fujimura, DFG (209) 948-7094 Predator densities/ population measurements for predatory fish in CCF, using Petersen mark-recapture techniques. Attempts at making these estimates were suspended after August 1994, may resume in the future pending further information (studies) on CCF striped bass movement and recruitment (see below).

Predator food habits and growth rates in CCF. These studies are ongoing, providing basic information on piscivorous fish prey preferences and selectivity. Scale reading for age/growth determination has been suspended pending fish movement studies to determine whether CCF striped bass represent a distinct population or a population in constant flux with fish community outside the forebay.

CPUE studies to monitor seasonal densities and activity levels of predator size fish. Sampling efforts using standardized gill-net and hook-and-line gear were recently expanded for 1995. Bi-weekly sampling was increased to weekly sampling; day-time samples collected each week and night-time samples collected every other week. The objective of this sampling is to maintain a low-effort monitoring program for striped bass in CCF, to monitor fish activity and piscivorous feeding behavior. Given the movement of striped bass in and out of the forebay radial gates, a weekly sampling regime is warranted.

Striped bass sonic tagging and tracking studies will begin in July 1995, conducted quarterly into 1996. The objective is to gain a better understanding of the movement activities of predator size striped bass that occur in CCF. The goal is to determine if CCF striped bass are a true population, functionally contained within the forebay or not, and the seasonal trends in the fish population size and movement patterns that can effect predator control efforts.

During one or more drain-downs of the salvage facility secondary channel, predator size striped bass 250 mm fork length and up will be tagged with Petersen disk tags prior to trucking and releasing the fish in the lower Delta. The objective is to tag enough striped bass (numbers exceeding 200 are commonly removed during drain-downs), to detect whether they return to CCF after release in the lower Delta. The ultimate goal of this tagging is to better understand the recruitment mechanisms (in conjunction with other monitoring above), and how salvage and relocation activities may be improved to minimize entrainment losses at CCF.

Clifton Court Forebay Temperature

Contact Person: Ted Sommer, DWR (916) 227-7537

Real time temperature monitoring using 15 minute interval recording thermometers in the northern most portion of the forebay and at DWR Station #2, to be maintained by DFG (previous monitoring was conducted by DWR and focused at the outlet channel, the inlet channel, and at DWR Station #2, located roughly half-way in-between). Infrared water temperature, flow patterns, and turbidity images from NASA flight surveys over CCF, to provide "real-time" data on the entire forebay from an aerial perspective.

H. EXISTING FISH FACILITIES EVALUATION

Contact Person: Scott Barrow, DFG (209) 948-7097

Both the CVP's and the SWP's Delta water export facilities include fish protective facilities consisting of screens, bypasses, holding tanks, and trucking facilities to salvage fish from exported water. The SWP's John E. Skinner Delta Fish Protective Facilities (SDFPF) was the subject of a major evaluation shortly after it construction in the late 1960's to establish operating criteria and evaluations have continued at a lower level since then. The nearly 40 year-old Tracy Fish Collection Facility (TFCF) is presently undergoing a major efficiency evaluation in order to identify appropriate measures to upgrade and improve the facility. A description of current facility evaluations follows.

In addition to the evaluations of the TFCF and SDFPF, this section of the report includes brief descriptions of fishery impact evaluations being conducted in relation to the operations of the Suisun Marsh Salinity Control Structure and the South Delta Temporary Barriers Project. These elements also are described below.

SDFPF Evaluation:

Previous work for this element has documented the screen efficiency of the SDFPF and established operational criteria, such as screen approach velocity and handling and trucking procedures, to maximize efficiency for certain species, particularly salmon and striped bass. Two methods have recently been implemented to increase salvage efficiency in response to the listing of winter-run chinook salmon and delta smelt. These are predator removals from the secondary channel systems to reduce the buildup of predatory fish and more frequent fish hauling to the release sites to reduce holding time in the holding tanks. A complete facility evaluation study plan is under development to respond to issues raised in the biological opinions of delta smelt and winter-run, and investigations have been initiated, as follows.

SDFPF Handling and Trucking Evaluation Handling and trucking mortality rates for delta smelt and splittail are unknown, and it is important to understand if these special status species survive the fish facility salvage operations. Recently, an experimental facility was developed in the old holding tank building of the SDFPF to conduct pilot studies of smelt and splittail handling and trucking mortality. The pilot studies have so far involved the removal and holding of small numbers adult smelt from various phases of the salvage process to identify major sources of mortality and try different experimental procedures. Similar pilot studies will be conducted with juvenile smelt during the summer of 1995. The results of the adult smelt work are now being evaluated.

Evaluation - Enhancement of Fish Passage Through the Secondary Channels

New holding tanks were added to the SDFPF in 1992, and subsequent simultaneous operation of the new and old secondary systems suggest that the new secondary system is less efficient than the old secondary system. Inadequate flows velocities into the bypass pipes leading toward the holding tank buildings are suspected to be the problem. Salvage data are now being analyzed to confirm the apparent relative inefficiency of the new secondary system. We suspect that during hours of darkness fish are more willing to enter the bypass pipes because they are not passing from a light to dark environment. For this reason a study is planned to cover the secondary to see if this improves fish passage rates during daylight hours. An experimental canvas cover system have been received, and the design of the framework to support the cover over the new secondary channel is under development.

TFCF Investigations for Increasing Salvage Efficiencies and Assessing Fishery Opportunities The TFCF is not attaining the desired efficiencies originally envisioned. A number of improvements may be possible and are being investigated to lessen direct fish losses. Recent investigations have revealed that primary and secondary louver efficiencies can be decreased as much as 50 percent with increased debris loads. New flow monitoring equipment is being installed. A study proposal is being developed for evaluating the entire TFCF, and an "Overview Report" is under development to guide long term research and facility improvement activities.

Delta Fish Facilities Salvage Monitoring Program

Contact Person: Jane Arnold, DFG (209) 942-6109

The work in this element documents the entrainment of delta fish species at the SDFPF and TFCF due to water exports from the South Delta. The entrainment is monitored 24 hours a day whenever the SWP and CVP pumping plants are exporting water. The two fish facilities have bi-hourly species sub-sampling with four length measurement samples per day. The salvaged fish are trucked daily to several release sites in the western Delta, and the schedule of fish hauling dependent on salvage rates, debris loading, and special listed species procedures. The data from the salvage sampling is keypunched daily and salvage and loss estimates are generated and distributed as required. The SDFPF salvage sampling and fish hauling are performed by DFG personnel, and TFCF salvage sampling and fish hauling are done by USBR personnel. The Delta Fish Facilities Salvage Program is the source for daily salvage and loss estimates for the monitoring of incidental take of listed fish species by southern delta water exports.

Suisun Marsh Salinity Control Structure (SMSCS) Adult Salmon Migration Evaluation:
Contact Person: George Edwards, DFG (209) 948-7096

The U.S. Army Corps of Engineers (COE) permit for the SMSCS required an evaluation of the effects of the barrier on fish migration. Early studies suggested that the barrier may delay the upstream migration of adult salmon. The barrier is in place and operating during the adult winter-run migration season (February-April) so more intensive studies were requested by NMFS and DFG. Because winter-run are so few in number, studies were conducted in the fall of 1993 and 1994 (and are planned for the fall of 1995) using fall-run as surrogates for winter-run. During each of the SMSCS's three operating modes, 15-20 adult salmon are captured downstream of the structure with gill-nets, fixed with sonic tags, and their migration past the structure monitored using fixed and mobile receivers.

South Delta Temporary Barriers Project Fishery Evaluation:
Contact Person: Mike Healey, DFG (209) 948-7800

DWR's and USBR's south delta temporary barriers project involves the experimental placement of seasonal rock water- elevation control structures in Middle River, Old River, and Grantline Canal near Tracy. Included in the COE permit and the delta smelt and winter-run biological opinions for the project are requirements for the evaluation of potential project fishery effects. The evaluation is its fifth and perhaps final year. The fishery effects evaluation includes monthly sampling at 16 barrier-influenced and reference sites via hoop-nets and electrofishing. Sampling for adult salmon by drift gill-net during the month of September is also conducted to detect any delay or blockage of their upstream migration