Biota are shifting their phenologies in response to changing climates. However, the magnitude and direction of these shifts can differ among trophic groups, potentially decoupling food webs when patterns diverge. Moreover, phenological responses to environmental cues are often assumed to be static, but this assumption may misrepresent future dynamics as phenological plasticity can vary over time and responses may change under novel climatic conditions. Here, we assessed the time-varying drivers of phenological change for fishes and their zooplankton prey in the San Francisco Estuary. We found that phenological shifts were common across the community (22.4% of taxa), but trends diverged between trophic guilds, with zooplankton peaking earlier in the year (-0.95 ± 1.29 days per year) while fishes often peaked later (.046 ± .9). Additionally, multivariate dynamic linear models indicate that phenology/environment relationships were non-static, with responses to temperature, salinity, and secchi changing in magnitude and, in some cases, direction throughout the time series. When we compared historical sensitivities to patterns within the last decade, we found that the environment is increasingly driving phenological change with recent phenological sensitivities being higher in 38.1% of fish time series and 37.9% of zooplankton time series. Taken together, our findings suggest that phenological responses are accelerating, with time-varying sensitivities and differential shifts between trophic groups amplifying the risk of trophic mismatches. Thus, accounting for temporally variable responses is critical to anticipating how climate change will affect species interactions and ecosystem function.