Community Patterns and Environmental Associations for the Early Life Stages of Fishes in a Highly Transformed Estuary

Estuaries are important fish nursery areas, yet little is known of how environmental forcing influences estuarine fishes during their early life stages. We analyzed environmental and larval-juvenile fish community data in the upper San Francisco Estuary (SFE) from spring to early summer 1995-2017, to better understand drivers of spatiotemporal community patterns in this highly modified estuary. We evaluated community patterns based on the relative abundance and diversity of native and introduced fish in the SFE and their predominant distribution (pelagic, demersal). The upper SFE experienced a downward trend of freshwater outflow and upward trends of temperature and salinity intrusion. Fish relative abundance only showed long-term downtrends for native and introduced pelagic fish groups. The most influential habitat components for relative abundance and diversity of fish groups were in decreasing order: temperature, salinity, Secchi depth, bottom depth, and zooplankton biomass. Early life stages of native and introduced fishes were generally segregated spatially and temporally, with native fishes more associated with cooler, saltier, and higher turbidity habitats during early to mid-spring compared to introduced fishes during late spring to early summer. Community ordination showed that environmental (temperature, salinity, outflow, Secchi depth, and zooplankton biomass) and spatiotemporal factors (month and depth), explained nearly 40% of the total variance. Our results suggest that the shorter duration of planktonic and nektonic stages of demersal fish groups results in higher resiliency compared to pelagic fishes. The declining abundance of pelagic fishes overall seems to be linked to drought effects and human-induced synergistic interactions intensified by climate change.