Fish surveys in the estuary: the whole is greater than the sum of its parts

by Dylan K. Stompe, Peter Moyle, Avery Kruger, John Durand

Fig. 1. Measuring a Sacramento splittail caught in a bottom trawl, Suisun Marsh. Photo: Peter Moyle

The San Francisco Estuary is a dynamic and altered estuary that supports a high diversity of fishes, both native and non-native. These species have substantial recreational, commercial, and intrinsic value to people. Since the 1950s, various agencies and UC Davis have established long-term surveys to track the status of fish populations. These surveys help scientists understand how fishes are responding to natural- and human-caused changes to the Estuary.

Each survey has strengths and weaknesses due to differences in sampling gear and effort, program duration, consistency of sampling, and area sampled. Because of this, it is challenging to understand drivers of change when looking at only a single survey. For example, when considering a single survey with limited sampling area, a decline in catch may be associated with either A) change in the distribution of a species within the Estuary, B) change in characteristics of sampling sites (e.g., deepening or shallowing, invasion of submersed aquatic vegetation) that affects gear efficiency, or C) a true decline in the Estuary-wide abundance of a species.

Surveys are designed to catch different species based on the question under investigation.  Common gear types include midwater trawls, bottom trawls, and beach seines, and each one is better at catching certain species than others (Figure 2). Midwater trawls are generally best at catching pelagic fishes such as juvenile salmon, striped bass, and smelt; bottom trawls do a better job of catching benthic fishes such as Sacramento splittail and gobies; and beach seines are best at catching fishes associated with shallow or weedy-edge habitats, such as largemouth bass and Mississippi silverside.

Fig. 2. Illustration of gear types used in San Francisco Estuary fish surveys.

One of the oldest and most widely cited surveys in the Estuary is the California Department of Fish and Wildlife Fall Midwater Trawl Survey, which was designed primarily to identify trends in striped bass populations. Thankfully, other fish species captured in this and other surveys are recorded as well. As a result, numerous papers have been published identifying periods of declining catch of native and non-native pelagic fishes leveraging the Fall Midwater Trawl data set. However, when data from other surveys are considered, different stories emerge.

We combined data from 14 long-term surveys (Table 1) in a way that allows for basic analysis of trends for up to 167 fish species in a much more spatially and temporally rich manner than could be done with a single survey (Stompe et al. 2020). These surveys use different methods and sample different areas so the total number of fish that they catch is not comparable. However, the trends in catch are comparable among surveys. Using data from multiple surveys in combination shows that some trends for fishes that are present in some surveys are absent or even contradicted by others (Figure 3, 4).

Fig. 3. Trends in pelagic fish catch per unit effort (CPUE) as show by the CDFW Fall Midwater Trawl (right) and aggregative data (left). Notice wide fluctuations in longfin smelt CPUE in the Fall Midwater Trawl versus consistent decline in aggregative data, as well as the steep decline in threadfin shad catch around the year 2001 in Fall Midwater Trawl versus consistent catch in aggregative data. Note that both sets of data show a decline in pelagic fishes in general starting around 1980, followed by a partial recovery, and then another decline starting in about 2001.  Mean annual CPUE calculate as the average catch per trawl or seine pull every year. The blue line denotes the approximate year of invasion by overbite clam, while the red line represents the initiation of the Pelagic Organism Decline (POD, Sommer et al. 2007, Thomson et al. 2010). The horizontal black bars show periods of drought.

For example, average catch per trawl of threadfin shad by the Fall Midwater Trawl declines drastically between 2001 and 2002 (Figure 3, panel B). However, aggregated data revealed that the population did not decline during this time period, and in fact remained relatively stable up until 2007 (Figure 3, panel A; see Stompe et al. 2020 for aggregation methods). The expanded data suggest that the decline in catch per trawl by the Fall Midwater Trawl between 2001 and 2002 was likely the result of changes in threadfin shad distribution or behavior, or changes in sampling station characteristics.

Similarly, if we consider catch per trawl of striped bass in two dissimilar surveys within the Estuary, very different trends appear. Average catch of striped bass per trawl by the Fall Midwater Trawl declines to near zero by the year 2000, while average catch per trawl remains relatively high throughout this same time period in the Suisun Marsh Otter Trawl (Figure 4). The Suisun Marsh Otter Trawl primarily samples shallow and marshy habitats as opposed to many of the deeper and less productive waters sampled by the Fall Midwater Trawl. This differential indicates productive areas such as Suisun Marsh are likely functioning as important and resilient refuges for the fishes of the Estuary.


Fig. 4. Average catch per trawl, by year, of striped bass in the Fall Midwater Trawl (FMWT) and the Suisun Marsh Otter Trawl (SMOT) surveys. Notice how catch by the FMWT declines to near zero by the year 2000 but remains relatively high (yet variable) in the SMOT.

Knowing how species move within the Estuary and what habitats become productive or unproductive over time allows us to make better-informed and more effective management decisions. Each unique survey of the Estuary is an important key to our understanding of fish populations. While certain surveys may appear to have more utility right now, it is impossible to predict which surveys will become invaluable as the Estuary continues to change, new fish species are inevitably listed under the state and federal endangered species acts, and new alien species invade.

Further Reading:

Stompe D.K., Moyle P.B., Kruger A., Durand J.R. 2020. Comparing and Integrating Fish Surveys in the San Francisco Estuary: Why Diverse Long-Term Monitoring Programs are Important. San Francisco Estuary and Watershed Science, 18(2).

Sommer T., Armor C., Baxter R., Breuer R., Brown L., Chotkowski M., Culberson S., Feyrer F., Gingras M., Herbold B., Kimmerer W. 2007. The collapse of pelagic fishes in the upper San Francisco Estuary. Fisheries, 32(6):270-277.

Thomson J.R., Kimmerer W.J., Brown L.R., Newman K.B., Nally R.M., Bennett W.A., Feyrer F., Fleishman, E. 2010. Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary. Ecological Applications, 20(5):1431-14

This work came from a recently published paper comparing and integrating fish surveys in the SF Estuary (Stompe et al. 2020). It is part of a larger project to evaluate striped bass demography and natural history in the Estuary, funded by California Department of Water Resources.

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