Delta Juvenile Fish Monitoring Program

Program Overview

The Delta Juvenile Fish Monitoring Program (DJFMP) administers several long-term and directed fish monitoring projects within the Sacramento-San Joaquin Delta and San Francisco Bay. The DJFMP was initially established in the 1970s to monitor juvenile fall-run Chinook Salmon Oncorhynchus tshawytscha abundance, and to investigate how reduced river flows might affect the survival of young salmon. Today, year-round monitoring continues with an emphasis on populations of all races of Chinook Salmon, Delta Smelt Hypomesus transpacificus, and other Delta resident fish.

History

1970s: DJFMP begins monitoring salmonid abundance and conducting mark-recapture studies to determine how river flows, diversions, and abiotic factors affect juvenile salmon survival.
1982: DJFMP adjusts monitoring to evaluate the impact of through-Delta water conveyance on juvenile salmon survival.
1992–1993: Endangered Species Act listing of Sacramento River winter-run Chinook Salmon.
1998–1999: Central Valley Steelhead O. mykiss and spring-run Chinook Salmon are federally listed as threatened. DJFMP initiates year-round sampling at and between the entry (Sacramento and Mossdale) and exit (Chipps Island) points of the Delta and in the San Francisco Bay.
2000: The Vernalis Adaptive Management Plan (VAMP) is initiated as part of the State Water Resources Control Board 1995 Water Quality Control Plan. VAMP aims to determine survival of and protect juvenile salmon as fish originating in the San Joaquin River migrate through the Delta. DJFMP supports VAMP by tagging and releasing juvenile salmonids in the South Delta each year until 2011.
2011: The National Marine Fisheries Service drafts a salmon decision process (NMFS 2011, Action IV.1.2) to minimize the impact of the Delta Cross Channel on emigrating salmonids and Green Sturgeon Acipenser medirostris. This process includes the Sacramento Catch Index, which is generated from beach seine and trawl catch data collected by the DJFMP on the Sacramento River. Last year of fish tagging and release for VAMP.
2012: DJFMP continues yearly acoustic tagging and release of Chinook Salmon and steelhead in the South Delta to estimate juvenile salmonid survival.
2013: Year-round beach seining and spring larval trawling within Liberty Island is incorporated into regular sampling.
2016: Trawling is increased to 5–7 days per week at Sacramento and Chipps Island trawl sites during the winter and spring to improve estimates of population abundances for juvenile Chinook Salmon.

Current Methods

Midwater and Kodiak Trawling

The DJFMP primarily uses midwater or Kodiak nets to trawl for juvenile fish at the entry and exit points of the Delta. A midwater net is used at the Chipps Island Trawl Site, a Kodiak net is used at the Mossdale Trawl Site, and both types of nets are used at the Sacramento Trawl Site depending on the time of year.

Both Kodiak and midwater nets are pulled along the surface of the water for the duration of the tow. Kodiak trawls are conducted with two vessels—a chase boat and a net boat. Each net is composed of panels with different mesh sizes. Mesh size decreases as panels move from the mouth to the cod end of the net. Midwater trawls are closed with a tie, while Kodiak nets have a live box attached to the end. The live box contains internal baffles intended to minimize fish mortality and stress due to flow pressure. See Table 1 for net size specifics.

Left panel: two crewmembers hauling a midwater trawl net in from the water. Right panel: two small boats, each with two to three people on board, pulling a Kodiak trawl net.

Sampling is typically conducted 3 times per week at each trawl site, except during the winter and early spring when sampling is increased at the Chipps Island and Sacramento trawl sites to 5–7 days per week. The increased sampling is intended to improve estimates of trawling efficiency and population abundances for fall-, winter-, and spring-run juvenile Chinook Salmon through capture of marked fish and genetic race identification of juvenile salmonid catches. During each sampling day, there are typically ten 20-minute tows conducted at each site.

Table 1 - Description of the primary nets used by the DJFMP to trawl for juvenile fish.
Net type	Where and when used	# of panels	Mesh size	Mouth size (fully extended)
Kodiak net	Mossdale year-round	5	5.1cm stretch at the mouth to 0.6cm stretch just before the live box	1.96 by 7.62m
Kodiak net	Sacramento October-March	5		1.96 by 7.62m
Large midwater net	Chipps Island year-round	5	10.2cm stretch at the mouth to 2.5cm stretch just before the cod end	7.64 by 9.65m
Small midwater net	Sacramento April-September	6	0.3cm stretch at the mouth to 0.6cm stretch just before the cod end	4.15 by 5m

Beach Seining

DJFMP crew members sampling for juvenile fish using a beach seine - two people wearing waders standing on the shore and pulling in a large net by hand. A grey tub and two white buckets are on the shoreline in front of the mouth of the net.

The DJFMP conducts weekly beach seining throughout the lower Sacramento and San Joaquin rivers, Liberty Island, and San Francisco Bay to monitor the relative abundance and distribution of juvenile Chinook Salmon and Delta resident fish in unobstructed near-shore habitats.

There are a total of 79 beach seine sites distributed across 8 regions. The DJFMP uses a 15.2 x 1.3 m beach seine net with 3 mm delta square mesh, a 1.2 m bag in the center of the net, and a float line and lead line attached to 1.8 m tall wooden poles on each side. In general, beach seines are deployed along the shoreline by two crew members within unobstructed habitats including boat ramps, mud banks, and sandy beaches.

Larval and Zooplankton Trawling

Larval trawl net as it is pulled alongside boat gunnel at Liberty Island - a small net mostly submerged and connected to a metal bar sticking out over the side of the boat.

The DJFMP samples for larval fish and zooplankton within and around Liberty Island to document the temporal and spatial distribution of native and non-native fishes in a naturally-restoring tidal wetland. Sampling is conducted between February and June to encompass the potential spawning and rearing seasons for several species of fish. Sampling is mostly conducted at high tide to allow access to minimum trawling depths, and is randomly conducted during flood or ebb tide.

A 500 µm larval net is used to collect larval fish, and a 50 µm net is used to collect zooplankton for potential analyses on prey availability. Ten trawls are conducted one day per month at randomly-chosen sites within each of the northern and southern portions of the island. There is also one day per month that includes 9 fixed sites on the outside of the island. At each site, two larval nets are deployed concurrently on either side of the boat, resulting in two replicate samples per site. Larval trawls are generally 10 min in duration. One zooplankton net is also deployed concurrently during one minute of each larval trawl.

After collection, each larval and zooplankton sample is rinsed into a sample bottle containing a solution of 10% buffered formalin and Rose-Bengal for preservation and tissue staining. Samples are then transferred to the DJFMP lab for sorting and identification of larval fish.

Publication Highlights

Brandes, P., K. Perry, E. Chappell, J. McLain, S. Greene, R. Sitts, D. McEwan, and M. Chotkowski. 2000. Delta Salmon Project Work Team Delta Juvenile Salmon Monitoring Program review. Interagency Ecological Program, Sacramento, California.
Brandes, P. L., and J. S. McLain. 2001. Juvenile Chinook Salmon abundance, distribution, and survival in the Sacramento-San Joaquin Estuary. Pages 39–136 in Brown R. L., editor. Contributions to the Biology of Central Valley Salmonids. California Department of Fish and Game Fish Bulletin 179(2).
Buchanan, R. A., P. L. Brandes, and J. R. Skalski. Survival of juvenile fall‐run Chinook Salmon through the San Joaquin River Delta, California, 2010–2015. North American Journal of Fisheries Management 38(3): 663–679.
Dekar, M., P. Brandes, J. Kirsch, L. Smith, J. Speegle, P. Cadrett, and M. Marshall. 2013. USFWS Delta Juvenile Fish Monitoring Program review. U.S. Fish and Wildlife Service, Background Report Prepared for Review by the Interagency Ecological Program Science Advisory Group, Lodi, California.
IEP SAG (Interagency Ecological Program Science Advisory Group). 2013. Review of the IEP Delta Juvenile Fishes Monitoring Program and Delta Juvenile Salmonid Survival Studies. IEP SAG, Summary Report, Sacramento, California.
Mahardja, B., M. J. Farruggia, B. Schreier, and T. Sommer. 2017. Evidence of a shift in the littoral fish community of the Sacramento-San Joaquin Delta. PLoS ONE 1(12):e0170683.