Native Fish

The Native Fish Indicator provides insights into the status and trends of native fish populations in the San Francisco Estuary, reflecting the health of aquatic habitats and the ecological processes that sustain them. Natural ecosystems that function properly support healthy fish communities. Habitat degradation, water pollution, diminished freshwater flows, non-native species, and extreme weather events, among other stressors, can cause declines in the native fish community. The Native Fish Indicator can inform management actions to restore and maintain ecological resilience in the Bay-Delta system, which is integral to California’s water supply and biodiversity.

In recent years, results have shown Good and stable conditions for native pelagic (found higher in the water column) and demersal (found lower in the water column) fishes in open-water Bay habitats. In contrast, conditions remain Poor in the open-water, littoral, and wetland regions of the Delta and Suisun Bay. However, shoreline surveys have shown recent improvements in native fish abundance in the nearshore “beach zone” of the Delta in 2023, a wet year following several drought years. This suggests that, despite Delta fish doing poorly overall, some populations may still have enough resilience to respond positively to favorable conditions, such as increased freshwater inflow and wetland restoration.

The native fish communities of the Bay and Delta were assessed using different long-term monitoring surveys. The Bay fish community was sampled with trawls that collected fish in open water habitats (pelagic and benthic), so the current Bay Fish Index doesn’t include fish using shoreline or wetland habitats. As wetland restoration in the Bay expands, future iterations of the indicator will aim to incorporate new Bay wetland fish monitoring survey data. The Delta Fish Index, by contrast, includes both open-water and nearshore “beach zone” habitats, as well as Suisun Marsh, reflecting conditions in the littoral zone and wetlands, as well as offshore areas.

Stressors such as declining freshwater inflow, invasive species, pollution, and extreme weather events are major stressors likely reducing fish survival, particularly in the Delta (Sommer et al. 2007; Light and Marchetti 2007). Water diversions and altered flow regimes continue to impact fish distributions and abundance (Jassby et al. 1995; Kimmerer 2002). Additionally, warming temperatures, changing salinity levels, and increased harmful algal blooms pose growing threats to fish populations.

Efforts to support native fish populations include wetland restoration, flow management, pollution reduction, conservation culture programs, and Endangered Species Act protections. The Bay and Delta restoration initiatives aim to improve habitat conditions, but large-scale ecosystem recovery remains complex due to competing water demands and uncertain future weather scenarios. Despite targeted interventions, challenges persist. Water diversions, habitat fragmentation, and competition and predation by non-native species continue to pressure native fish populations. The interplay between hydrodynamics, food web shifts, and environmental stressors makes it difficult to reverse long-term declines without comprehensive, system-wide management.

Estuarine fish are impacted by many features of the Estuary, including water quality, freshwater flows, and habitat condition, which together shape the ecological health of the Bay-Delta Estuary for native species. Long-term declines in native fish abundance mirror broader environmental trends, reinforcing the need for coordinated, science-based management. Future efforts aim to include additional data on fish in wetland habitats across the Estuary, provided by the Wetlands Regional Monitoring Program.