A Spatiotemporal History of Key Pelagic Fish Species in the San Francisco Estuary, CA

Estuaries across the globe have been subject to extensive abiotic and biotic changes and are often monitored to track trends in species abundance. The San Francisco Estuary has been deeply altered by anthropogenic factors, which is reflected in substantial declines in some native and introduced fishes. To track trends in fish abundance, a multitude of monitoring programs have conducted regular fish surveys, some dating back to the late 1950s. While these surveys are all designed to track population-scale changes in fish abundance, they are methodologically distinct, with different target species, varying spatial coverage and sampling frequency, and different gear types. To compensate for individual survey limitations, we modeled pelagic fish distributions with integrated data from many sampling programs. We fit binomial generalized linear mixed models with spatial and spatiotemporal random effects to map annual trends in the spatially explicit detection probabilities of striped bass, Delta smelt, longfin smelt, threadfin shad, and American shad for the years 1980 to 2017. Overall, detection probability has declined by approximately 50% for striped bass and is now near zero for the two smelt species, while threadfin shad and American shad have both experienced fluctuations with only slightly reduced detection probabilities by 2017. Detection probabilities decreased dramatically for these fishes in the Central and South Delta, especially after the year 2000. In contrast, Suisun Marsh and the North Delta acted as refuge habitats with reduced levels of decline or even increased detection probabilities for some species. Our modeling approach, using disparate datasets, demonstrates the simultaneous spatially driven decline of pelagic fish species in a highly altered estuary.