Suisun Marsh fishes in 2020: Persistence during the Pandemic

by Teejay O’Rear, John Durand, Peter Moyle

Two fishes that rely on Suisun Marsh for persistence in the San Francisco Estuary: striped bass and Sacramento splittail

Suisun Marsh is central to the health of the San Francisco Estuary. Not only is it a huge (470 km2) tidal marsh in the center the northern estuary (Figure 1), but it is an extremely important nursery area for species such as splittail, striped bass, longfin smelt, and, formerly, delta smelt. Since January 1980, a team from The University of California, Davis, in partnership with the California Department of Water Resources (DWR), has systematically monitored the marsh’s fish populations. The team had been sampling the fish and invertebrates every month with trawls and beach seines, with a nearly unbroken record. Then Covid-19 restrictions settled in, making it hard to continue sampling with a crew of four people in a 19-ft boat. How does one maintain a six-foot distance and still operate the boat and sampling nets? After a two-month hiatus in sampling, a solution was found: do the sampling with just two experienced people. The two-person crew was led each month by Teejay O’Rear, the highly experienced field manager of the Suisun Marsh project. Sampling took three exhausting days, but the data stream continued its flow. The following is a brief summary of what they learned about the marsh in 2020.

Figure 1. Suisun Marsh study area (“GYSO” = Goodyear Slough Outfall, “MIDS” = Morrow Island Distribution System, “RRDS” = Roaring River Distribution System, “SMSCG” = Suisun Marsh Salinity Control Gates, and “WWTP” = the Fairfield-Suisun Sanitation District’s wastewater treatment plant discharge point into Boynton Slough; map by Amber Manfree).

After the wet year of 2019, Suisun Marsh was subjected to very dry conditions in 2020. Delta outflow was lower than average throughout the year (and accompanied by little floodplain inundation), resulting in higher-than-average salinities. Two increasingly common conditions recurred in 2020: water was warmer than average (Figure 2), and clearer than average in summer and autumn.

Figure 2. Monthly average water temperature in Suisun Marsh in 2020 and for all years of the study (1980 – 2020); error bars are standard deviations in 2020 (* = no samples). See O’Rear et al. 2021 for details.

Fish catches in Suisun Marsh in 2020 reinforced three common observations: (1) lower flows and higher salinities are unfavorable for many common marsh fishes, whether native or non-native; (2) small, dead-end sloughs are key for supporting abundant fish populations; and (3) Suisun Marsh is disproportionately valuable to fishes of conservation importance. Nearly all fish species, both native and non-native, were less abundant than usual in 2020, especially those needing fresh water to spawn (Figure 3). In particular, the native, floodplain-spawning Sacramento splittail and non-native fishes that eat zooplankton and spawn in fresh water [threadfin shad, American shad, and striped bass] had reduced numbers. However, their numbers were relatively higher in Suisun Marsh than in the rest of the estuary. The frequently high numbers of all four species in Suisun Marsh since the early 2000s are notable given they are coincident with estuary-wide declines in plankton productivity and chronically low abundnaces of pelagic fishes in the estuary’s main rivers and bays (the “Pelagic Organism Decline”; Sommer et al. 2007). Many age-0 longfin smelt, a native zooplankton-eating species, were caught in Suisun Marsh in spring, which had not happened since 2013. Large fish catches most frequently occurred in small, dead-end sloughs where plankton concentrations are usually higher. Overall, Suisun Marsh is crucial for sustaining populations of valuable fishes, both native and non-native, particularly zooplanktivorous fishes and Sacramento splittail. The general pattern of native and non-native fish species responding in similar ways to environmental change suggests development of a novel ecosystem composed of species from all over the world (Figure 3; Aguilar-Medrano et al. 2019).

Figure 3. Annual average catch per trawl of native and non-native species in Suisun Marsh, 1980-2020.

We conclude with a discussion of two fish species that seem especially dependent on conditions in Suisun Marsh: Sacramento splittail and juvenile striped bass. 

Sacramento Splittail

Figure 4. Annual catches per trawl of three ages classes of Sacramento splittail in Suisun Marsh, 1980-2020. 

The splittail is a native minnow that spawns in areas that flood during winter months, especially the Yolo Bypass and Cosumnes River. Juveniles rear on flooded vegetation but emigrate en masse as water levels drop and move down the Sacramento River. Many, if not most, juveniles wind up in Suisun Marsh, when they are 40-50 mm long. They rear in the marsh for 2-3 years, until maturity, and then migrate with older fish to the spawning areas. They are repeat spawners, living 7-9 years. While splittail presumably once spawned and reared in many places in the rivers and estuary, today most of the population appears to spawn in the bypass and rear in Suisun Marsh, making them highly vulnerable to environmental change.

In the marsh, splittail numbers dropped considerably from 2019 to 2020, reflecting limited flooding. Nevertheless, catches were above average for the 40-year sampling period (Figure 4), reflecting in part a healthy adult population and quality rearing conditions in smaller sloughs for juveniles that did make it to the marsh. Extended drought may change this picture.

Striped Bass

Figure 5. Annual catch per trawl (purple squares) and catch per beach seine haul (red triangles) of striped bass. Most of the catch is young-of-year (age 0) bass. Figure from O’Rear et al. (2021).

Striped bass are not native but are one of the best indicators of ecological conditions because they complete their entire life history in the estuary watershed: they need healthy rivers, a healthy estuary, and a healthy coastal ocean to flourish. In our samples, striped bass catches consist mainly of young-of-year (age 0) individuals, but abundances plummeted in 2020 and were below average compared to all other years (Figure 5). Juvenile striped bass were most abundant in small sloughs, where planktonic food (i.e., opossum shrimp) was most abundant. The distribution and relatively low numbers of age-0 striped bass in 2020 was consistent with low flows in rivers supporting little successful spawning by adult bass and high zooplankton food in small, dead-end sloughs.


Sampling in Suisun Marsh has been the responsibility of many graduate students and others over the years, including Donald Baltz, Robert Daniels, Bruce Herbold, Lesa Meng, Scott Matern, Robert Schroeter, Patrick Crain, Alpa Wintzer, Sabra Purdy, and Brian Williamson. They have been assisted by literally hundreds of volunteers and student assistants. Huge thanks to Jacob Katz and Jacob Montgomery for their support in the tough year of 2020. We appreciate the continued support of the sampling program over the years by DWR. Randall Brown of DWR kept the program going during its early uncertain years. The views expressed in this report are those of the authors and do not reflect the official policy or position of DWR.

Further Reading

Aguilar-Medrano, R., J. R. Durand, V.H. Cruz-Escalona and P.B. Moyle. 2019. Fish functional groups in the San Francisco Estuary: understanding new fish assemblages in a highly altered estuarine ecosystem. Estuarine, Coastal and Shelf Science

Aha, N.M., P.B. Moyle, N.A. Fangue, A.L. Rypel, and J. R. Durand. 2021. Managed wetlands can benefit juvenile salmon in a tidal marsh. Estuaries and Coasts

Colombano, D.D., T.B. Handley, T. O’Rear, J.R. Durand, and P.B. Moyle 2021. Complex tidal marsh dynamics structure fish foraging patterns iin the San Francisco Estuary. Estuaries and Coasts. 

Colombano, D. D., J.M.Donovan, D.E. Ayers, T.A.O’Rear, and P.B. Moyle. 2020. Tidal effects on marsh habitat use by three fishes in the San Francisco Estuary. Environmental Biology of Fishes.

Colombano, D. D., A.D. Manfree, T. A. O’Rear, J.R. Durand, and P.B. Moyle. 2020. Estuarine-terrestrial habitat gradients enhance nursery function for resident and transient fishes in the San Francisco Estuary. Marine Ecology Progress Series 637: 141-157.

Moyle, P.B., A. D. Manfree, and P. L. Fiedler. 2014. Suisun Marsh: Ecological History and Possible Futures. Berkeley: University of California Press

O’Rear, T. A., J. Montgomery, P. B. Moyle, and J. R. Durand. 2021 (in review). Trends in Fish and Invertebrate Populations of Suisun Marsh, January 2020 – December 2020. Annual Report for the California Department of Water Resources Sacramento, California.

Sommer, T., C. Armor, R. Baxter, R. Breuer, L. Brown, M. Chotkowski, S. Culberson, F. Feyrer, M. Gingras, B. Herbold, W. Kimmerer, A. Mueller-Solger, and K. Souza. 2007. The collapse of pelagic fishes in the Upper San Francisco Estuary. Fisheries 32: 270-277.

Young, M., E. Howe, T. O’Rear, K. Berridge, and P. Moyle. 2020. Food web fuel differs across habitats and seasons of a tidal freshwater estuary. Estuaries and Coasts.

About andrewrypel

Andrew Rypel is an Associate Professor and the Peter B. Moyle and California Trout Chair of coldwater fish ecology at the University of California, Davis. He is a faculty member in the Department of Wildlife, Fish & Conservation Biology and Co-Director of the Center for Watershed Sciences.
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