River flow is an important component of estuarine ecology, delivering the freshwater and nutrients that drive physical characteristics and productivity of the ecosystem. Extreme events (droughts and high rainfall) can have profound effects on estuarine nekton communities. In the present study, we used a 19-year fisheries-independent monitoring time series (2001–2019) in combination with data on river flow to examine long-term patterns in nekton community structure in Apalachicola Bay and investigate the effects of Apalachicola River flow rate on observed changes in community structure. Analyses included lagged effects at 1-, 3-, 6-, and 12-month intervals. Results suggested episodic shifts in relative abundances of numerically dominant taxa with a relatively stable group of species occurring through time, however there was some evidence of serial change in community structure. Correlations of community structure with time revealed regular seasonality of species assemblages in the Apalachicola Bay system, which was strongly correlated with water temperature. Spatial structure (zones within the system) in nekton communities was correlated with salinity, water clarity, and depth. River flow rates affected community structure at 6- and 12-month time lags, but the magnitude of effects varied among gear types and spatial zones within the system. The most significant shifts in fish community structure occurred during drought years. Results suggest that long-term changes in flow regimes strong enough to alter spatial salinity patterns and distribution of habitat types could affect community structure of nekton in the Apalachicola Bay system.
