"View from the Water" Blog

By: Jillian Burns (CDFW), Environmental Scientist

The California Department of Fish and Wildlife’s (CDFW) San Francisco Bay Study (Bay Study) has collected a lot of data on fish, crabs, and shrimp in the San Francisco Estuary (Estuary)
since it began in 1980, but what does a day sampling on the water look like?

The survey crew is on the water 6-7 days a month, year-round, sampling at 52 stations (numbered by region; see Figure 1) throughout the Estuary including channel and shoal areas of the Sacramento and San Joaquin rivers, Suisun Bay, San Pablo Bay, Central Bay, and South Bay. In this post, I’ll take you through a field day in the busiest region during our busiest season: summer in the Central Bay when fish, crabs, and shrimp that spawned in winter and spring have grown large enough to be collected by our nets. Most photos shown in this post are from our June survey in 2021 and 2022.

Central Bay Sampling Locations

At the start of a Central Bay sampling day, the crew meets at the Berkeley Marina very early in the morning and disembarks on CDFW’s 42-foot RV Longfin (Figure 2). The station path starts just outside the marina (station #212), then to Treasure Island (#211) and Alcatraz (#213); next we motor north to the eastern side of Angel Island (#214) and continue sampling in the channel east of the Tiburon Peninsula (#215) and shoal east of Corte Madera (#244), then turn back towards the Berkeley Marina sampling just south of the Richmond-San Rafael Bridge and Red Rock Island (#216) and finish sampling at Southampton Shoal west of the city of Richmond (#243).

Crew Responsibilities

At each station, every member of the crew functions like a fine-tuned machine. The captain locates the towing location and decides on the tow direction based on the current and the amount of cable to deploy depending on the station depth; the deckhand and scientific aid deploy the nets making sure cables and doors don’t get tangled and the lead biologist records everything on a datasheet. We also collect water quality information e.g., a salinity and temperature profile of the entire water column using a SeaBird Electronics CTD (Figure 3).

Bay Study Trawl Methods

The Bay Study uses two trawling methods (midwater trawl and otter trawl), which target different habitats and species.

The midwater trawl (PDF) collects organisms that occur throughout the water column (i.e., pelagic; Figure 4), such as Northern Anchovy, American Shad (PDF), Pacific Herring, and Pacific Sardine, silversides (California Grunion, Jacksmelt, and Topsmelt), surfperches (Shiner Perch and Walleye Surfperch), and jellyfish (Figures 6 and 7). The midwater trawl net is set as deep as possible, near but not to the bottom, then is slowly retrieved for 8 minutes forming a diagonal line through the water column; finally, the last few minutes the net is towed at the surface.

The otter trawl collects bottom dwelling species (i.e., demersal; Figure 5) such as English Sole, Starry Flounder, California Halibut and other flatfishes, gobies, sculpins, crabs, and shrimp and is towed for 5 minutes (Figures 9 and 10). The otter trawl’s two 28.5-pound doors allow the net to ride along the estuary floor and a tickler chain at the mouth of the net displaces fish, shrimp, and crabs partially buried in the substrate. In that way, the otter trawl also gives us information about what makes up the bottom. We might pull up submerged aquatic vegetation, clams, oyster shells, and algae in addition to fish and crustaceans. However, there’s also a higher risk of snagging obstacles on the estuary floor, such as lost anchors or crab traps, or filling the net up with mud.

Processing the Catch

At the end of each tow, the net is emptied into a tub for processing the catch. Larger species like sharks, rays, skates, halibut, and sturgeon are measured and returned to the water immediately and we sort the remaining fish, shrimp, crabs, and jellyfish from debris. If large enough, halibut are sexed and tagged and when these fish are re-caught by recreational or commercial anglers, the location can be reported to CDFW to help managers understand the species’ movement. The fish and crabs from each tow are identified, counted, and a subset measured, while the jellyfish are identified and counted. A shrimp sample from the otter trawl is preserved to process in the lab. As we sample down the salinity gradient of the estuary, we can expect to encounter a wide range of species, whose composition, abundance, and distribution are also influenced by season, temperature, winter and spring freshwater outflow, ocean conditions (temperature, upwelling, currents), depth (channel or shoal), and other physical and biological variables. In Central Bay, we often catch visitors from the ocean that use the Estuary when conditions are right (e.g., Pacific Pompano and Curlfin Sole; Figures 8 and 11).

Bay Study Data and Its Uses

Data from the Bay Study and other IEP long-term monitoring programs have been used to describe impacts of introduced species, collapses in fish populations, shifts in the abundance and distributions of species, and responses of organisms to environmental change in the San Francisco Estuary (see Additional Reading below for some examples of these analyses). Managers who are interested in the status of protected species (e.g., the State threatened Longfin Smelt) and commercial and recreational fisheries (e.g., Pacific Herring, California Halibut, bay shrimp, and Dungeness crab) also use the data.

Stay tuned for more updates and stories from IEP on the water and follow IEP’s twitter updates. Also, check out a related post from the Science Stories: Adventures from the Bay-Delta Data blog about Bay Study's crab dataset.

Additional Reading

• Chapman J.W., Li J., McGowan M.F., Breitenstein R.A., Appy R., Hieb K.A., Piotrowski C.N., and Elder L.E. 2021. A doubled down invasion of the northeast Pacific by the Asian mud shrimp, Upogebia major and its coevolved bopyrid isopod parasite, Orthione griffenis (PDF). Aquatic Invasions 16(4): 721–749.
• Colombano, D. D., Carlson, S. M., Hobbs, J. A., and Ruhi, A. 2022. Four decades of climatic fluctuations and fish recruitment stability across a marine-freshwater gradient. Global Change Biology, 28: 5104– 5120.
• Kimmerer, W. J. 2006. Response of anchovies dampens effects of the invasive bivalve Corbula amurensis on the San Francisco Estuary foodweb (PDF). Marine Ecology Progress Series 324: 207-218.
• Martin, K. L. M., Hieb, K. A., and Roberts, D. A. 2013. A southern California icon surfs north: local ecotype of California Grunion Leuresthes tenuis (Atherinopsidae) revealed by multiple approaches during temporary habitat expansion into San Francisco Bay. Copeia 2013(4): 729-739.
• Sommer, T., Mejia, F., Hieb, K.A., Baxter, R., Loboschefsky, E., and Loge, F. 2011. Long-term shifts in the lateral distribution of age-0 striped bass in the San Francisco Estuary. Transactions American Fisheries Society 140:1451-1459.

USFWS Biological Science Technicians Billy Bullard (left) and Jordan Buxton (right) load gear boxes in preparation for a day of sampling on the Delta.


USFWS Mechanic Matt Myrick readies the R/V Threadfin for a day of sampling on the Delta.


USFWS Biological Science Technician Jacob Stagg throws a midwater trawl net into the water to begin daily sampling at the confluence of the Sacramento and San Joaquin Rivers.


Lodi Fish and Wildlife Office team members, preparing to leave for a day on the water, hold open a Kodiak trawl net.

By: Erin Sharkey, Biological Science Technician

It is another early morning, with clear skies and a slight Delta breeze in the forecast. The sound of a squeaky warehouse door continuously opening and closing can be heard from across the vast parking lot. Inside is a massive warehouse, shelves full of mysterious nets and gear. During these early morning hours, you can hear the tumbling thuds of gear boxes being collected.

U.S. Fish and Wildlife Service biological science technicians emerge from the warehouse and disperse into smaller groups. Some are foraging for baked goods out of small, white boxes; others are carrying boots, waders and various sampling gear. One in a standard brown uniform carries a beach seine net to the bed of a large pickup truck.

About 23 vehicles are needed to accomplish the monitoring and data-collecting efforts completed by the Lodi Fish and Wildlife Office every weekday of the calendar year. At the edge of the parking lot, small-watercraft operators and a mechanic are loading the largest research vessel in the fleet on a trailer. The R/V Threadfin is a solid 30-foot boat with a sturdy diesel, 6-cylinder engine to pull seriously large nets through the water over a long workday.

The Lodi Fish and Wildlife Office, one of the largest field offices in the Service, is a complex system of networks. The chain of command includes the head of the office, Project Leader Jeff McLain. Next up, we have Baker Holden, Lori Smith and Erin Strange, all formidable leaders who are essential for everyday coordination of this complex and dynamic operation. These four oversee multiple long-term monitoring efforts, special studies and restoration projects established for the conservation of native species in the San Francisco Bay Estuary and throughout the Sacramento River and San Joaquin River watersheds. 

There are four major programs based in the Lodi Fish and Wildlife Office. First is the Delta Juvenile Fish Monitoring Program, which began monitoring juvenile salmon in 1976. Next is the San Joaquin River Restoration Program, which has been working on Chinook Salmon restoration efforts since 2012. Third is the Enhanced Delta Smelt Monitoring Program, the new kid among the monitoring programs, beginning in 2017.Finally, the Anadromous Fish Restoration Program works to restore habitat and connectivity for fishes that migrate into and out of Central Valley tributaries. 

The four major programs are what keep the many biologists, administrative staff, technicians, mechanics and boat operators scurrying about. In addition, there is a slew of other special studies based out of the Lodi Office, from fish tracking to invertebrate sampling to computer modeling. All these activities result in the daily ballet of staff to achieve the mission of promoting native, self-sustaining ecosystems through leadership in anadromous fish restoration, and fisheries research and monitoring. 

Each program includes activities designed to monitor rare and endangered fishes, like Chinook Salmon or Delta Smelt, but also provides valuable information about habitat use and other fishes in the Sacramento and San Joaquin rivers and Delta. Sampling methods vary by program, target and even season. Sampling equipment includes a variety of different trawl nets, seine nets, electrofishing equipment, zooplankton nets and emergence traps (the list goes on!). The nets and traps filter water, like a whale feeding in the ocean, to catch aquatic organisms ranging from as small as fleas to as large as adult salmon and sturgeon. 

With so much sampling activity occurring on a daily basis, repairs are a part of the daily list of tasks to accomplish. Technicians and boat operators can often be seen taking out a Kodiak trawl net from the warehouse to inspect for any needed repairs. It is a massive net, 25 feet wide and 65 feet long. At the end is the live box (called the “cod end”), which allows fish to be safely captured and released back into the Delta after measurements have been recorded. Specialized tools are used to make the necessary repairs to ensure no fish are lost during a sampling effort. 

Follow along with future posts to learn more about field sampling and other work conducted by the Lodi Fish and Wildlife Office.

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Photo Credit: All USFWS photos taken by Erin Sharkey.