Remarkable Suisun Marsh: a bright spot for fish in the San Francisco Estuary

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by Teejay O’Rear and Peter Moyle

To most people, Suisun Marsh is either the seemingly blank area visible at 70 MPH from the north side of Highway 680 or the sudden expanse of tules visible after the Amtrak train leaves Suisun City, headed for Oakland. However, it is one of our favorite places in California, where it is easy to imagine being in a different place and time, with sturgeon jumping out of the water; flocks of ducks, ibis, and pelicans flying overhead; otters swimming by; and tule elk coming down to the water’s edge for a drink.  We know the marsh well because we have been taking a boat out every month to sample its fishes.  This sampling started 40 years ago, when Peter Moyle and a graduate student, Don Baltz, did some trawling in the marsh to look for tule perch and learned it supported many fish of all sorts.  Here we provide an updated account of Suisun Marsh fishes to show why the marsh is so important for conserving fishes in the upper San Francisco Estuary in general…and why we continue to be enthusiastic about working there.

Suisun Marsh is a brackish-water marsh bordering the northern edges of Suisun, Grizzly, and Honker bays in the San Francisco Estuary; it is the largest uninterrupted estuarine marsh remaining on the western coast of the contiguous United States. Much of the marsh area is diked wetlands managed for waterfowl, with the rest consisting of tidal sloughs, marsh plains, and grasslands. The marsh’s central location in the northern San Francisco Estuary makes it an important habitat for diverse freshwater, estuarine, and marine fishes.  The marsh also is a migratory corridor for anadromous fishes such as Chinook salmon and striped bass.

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Suisun Marsh (map by Amber Manfree).

The protection of Suisun Marsh was specifically written into the bill creating the State Water Project, mainly to ensure that waterfowl populations would not be harmed by increased diversions of fresh water.  Fish were also part of that protection, so in January 1980, the Department of Water Resources contracted with UC Davis to monitor fish populations in the marsh. The result was our Suisun Marsh Fish Study, which has consistently used beach seines and otter trawls to sample juveniles and adults of all species since the study’s inception.  The primary objectives of our study have included (1) evaluating effects on fishes of the Suisun Marsh Salinity Control Gates, which began operating in 1988; (2) examining long-term changes in Suisun Marsh’s ecosystem relative to other changes in the San Francisco Estuary; and (3) enhancing understanding of the life history and ecology of key species in the marsh.  Secondary objectives have included supporting research by other investigators through special collections; providing background information for in-depth studies of other aspects of the Suisun Marsh aquatic ecosystem, such as the feeding ecology of jellyfish; serving as a baseline for restoration projects; contributing to the general understanding of estuaries through publication of peer-reviewed papers; training undergraduate and graduate students in estuarine studies and fish sampling; and providing a way for managers, biologists, and anyone else interested in the marsh to experience it firsthand.

Pic 3 suisunThirty-nine years of annual otter trawl catches of the Suisun Marsh Fish Study, with key events noted. Note that catches of native and non-native fishes generally follow similar trends.

Our study has documented many patterns in the ecology of the fishes in both space and time. Moyle et al. (1986) evaluated the first five years of data and found three groups of fish species: one that was generally most abundant early in the calendar year (including small staghorn sculpin and starry flounder); another that was common in cool months (including threadfin shad, Delta smelt, and longfin smelt); and a third that was always present in the marsh, comprised of many species but dominated by Sacramento splittail, striped bass, and tule perch.  The species composition of the fish assemblage was relatively constant across years.  Native fishes were more prevalent in small, shallow sloughs, while non-native species were more prominent in large sloughs.

Total fish abundance declined across years because extremely favorable spawning and rearing conditions early in the study period were followed by both a drought and a major flood that resulted in poor recruitment (see figure).

Meng et al. (1994) incorporated eight more years into their analysis, which revealed that the composition of the fish assemblage was less constant over the longer period than the earlier study indicated. In addition, non-native fishes had become more common in small, shallow sloughs. This study also found a general decline in total fish abundance through time. The decreasing fish numbers appeared to be related to (1) drought and high salinities harming both native and non-native fishes, (2) effects of new invasions (e.g., overbite clam), and (3) increases in water diversions.

Eight years later, Matern et al. (2002) found results similar to Meng et al. (1994): fish diversity was highest in small sloughs, and fish abundances had fallen further.  However, since then, fish catches have often been higher, particularly in wet years. Notably, some fishes that have become scarce in the estuary’s main rivers and bays since the early 2000s have either increased (e.g., Sacramento splittail) or remained abundant (e.g., small striped bass) in Suisun Marsh.

While analyzing data collected in 2018, we noted the following trends in some key species:

Delta smelt.  For the third consecutive year, we caught no Delta smelt, providing further evidence that this species is approaching extinction in the wild.

Longfin smelt.  Numbers of this smelt remained very low, but a few were caught almost every month.

Threadfin shad.  This non-native shad is one of the most abundant plankton-feeding fish in the marsh with numbers that fluctuate greatly from year to year. Numbers seem to be gradually increasing from its lows in 1989-1995, with a peak in 2017.  Numbers in 2018 were considerably less than in 2017, but still in the top five years.

American shad.  Since 2001, the number of juvenile American shad, a non-native anadromous species, has gradually increased, roughly following abundance trends of threadfin shad, including record numbers caught in 2017.  This suggests that the two shad species are generally being affected by the same factors.

Striped bass juveniles are also non-native plankton feeders and are typically the most abundant fish in our trawl catches. They also had a peak in 2017, with a drop in 2018 to more typical numbers. However, the long-term trend in catch since 1980 is mildly downwards, with lots of erratic rises and falls from year to year.

Sacramento splittail is a native fish that spawns on floodplains upstream of the marsh but spends most of its time in the marsh feeding on invertebrates.  After a severe decline from 1980 to 1994, its numbers have steadily increased, with 2018 being the peak year for abundance.  We suspect that its continued increase through wet and dry years results from restoration actions on the Yolo Bypass and Cosumnes River floodplains coupled with favorable conditions in the marsh.


Sacramento splittail are native fish uncommon outside of Suisun Marsh, except when they leave to migrate upstream to spawn on floodplains. Photo by Teejay O’Rear

White catfish, a non-native, almost disappeared from Suisun Marsh during the 2012-2016 drought, because high salinities and low flows inhibited reproduction. High flows in 2017 did not replenish the population, so catches remained low in 2017 and 2018.

Mississippi silverside is an abundant non-native species that probably invaded the marsh just a few years before our study began. It hugs the edges of sloughs during the day and feeds on small invertebrates and larval fish. Numbers increased steadily to 2006 and then dropped to consistent, moderate levels.

Overall, 2018 was a modest year for native and other important fishes. After achieving very high numbers in the wet year of 2017 (see figure), fish abundances returned to more typical levels in 2018.  Non-native fishes dependent on plankton for part of their life cycle (American shad, threadfin shad, striped bass) declined from 2017 to 2018, but they were still relatively abundant in Suisun Marsh in contrast to the bays and large rivers of the estuary. However, native smelts were virtually absent in both Suisun Marsh and the main bays/rivers. The negligible smelt numbers and lower numbers of some other native fishes after 2017 (threespine stickleback, prickly sculpin) in Suisun Marsh were contrasted by the highest-ever abundance of Sacramento splittail.

In sum, the catches in 2018 highlighted:

  • the importance of flows and related salinities on fish abundance in Suisun Marsh, with higher flows generally yielding more fish, both native and non-native;
  • the disproportionate importance of Suisun Marsh for warm-water planktivorous fishes, especially striped bass juveniles;
  • the importance of the marsh as a nursery area for many species; and
  • the importance of Suisun Marsh as the estuary’s bastion for Sacramento splittail.

We continue to be fascinated by the dynamic nature of Suisun Marsh and the abundance of life it supports.  We also are improving our understanding of how diverse environmental factors, from droughts to operation of water projects, affect the marsh’s fishes. Our 40 years of study are likely to be especially useful in determining – and predicting – the effects of global climate change on the estuary and its fishes.

For more complete information see O’Rear et al. (2019). For an overview of Suisun Marsh, see Moyle et al. 2014.

Teejay O’Rear is a fish ecologist at the Center for Watershed Sciences. Peter B. Moyle is a UC Davis Professor Emeritus of fish biology and an associate director of the Center for Watershed Sciences.

Further reading

California Department of Fish and Wildlife. 2019. Trends in abundance of selected species. Available: (March 2019).

Matern, S. A., P. B. Moyle, and L. C. Pierce. 2002. Native and alien fishes in a California estuarine marsh: twenty-one years of changing assemblages. Transactions of the American Fisheries Society 131: 797-816.

Meng, L., P. B. Moyle, and B. Herbold. 1994. Changes in abundance and distribution of native and alien fishes of Suisun Marsh. Transactions of the American Fisheries Society 123: 498-507.

Moyle, P. B., R. A. Daniels, B. Herbold, and D. M. Baltz. 1986. Patterns in distribution and abundance of a noncoevolved assemblage of estuarine fishes in California. U. S. National Marine Fisheries Service Fishery Bulletin 84(1): 105-117.

Moyle, P. B., A. D. Manfree, and P. L. Fielder. 2014. Suisun Marsh: ecological history and possible futures. Oakland: University of California Press.

O’Rear, T. A., P. B. Moyle, and J. R. Durand. 2019. Suisun Marsh Fish Study: trends in fish and invertebrate populations of Suisun Marsh January 2017 – December 2017. California, California Department of Water Resources.  Available at:

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About jaylund

Professor of Civil and Environmental Engineering Director, Center for Watershed Sciences University of California - Davis
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2 Responses to Remarkable Suisun Marsh: a bright spot for fish in the San Francisco Estuary

  1. J Rizzi says:

    Reduce Importing Salt into Delta through the Dredged Shipping channel will help the Delta even more.

  2. Pingback: Striped Bass: An Important Indicator Species in the Delta | California WaterBlog

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