Historic climatic fluctuations in the San Francisco Bay region have been shown to significantly exceed those experienced since the advent of most European settlement 160 years ago. Meanwhile, anthropogenic climate change is predicted to have wide-ranging impacts on northern Californian climate regimes, including precipitation, yet the potential consequences of these and past changes are still quite unknown. Salinity, a key estuarine variable, is directly influenced by precipitation and is widely recognized as a potentially important factor governing community composition in estuaries. Using observational and experimental approaches, we assessed the effect of seasonal changes in water column conditions on community diversity over several years, including the success of native and non-native species. We examined correlations between sessile invertebrate recruitment and survival patterns and seasonal variation in salinity and temperature in San Francisco Bay. We then experimentally manipulated temperature and salinity levels to directly assess their effects on survival. We demonstrate that more extreme fluctuations even in today's more benign climate regime can have dramatic effects on estuarine communities, significantly altering the diversity, distribution, abundance, and timing of recruitment of estuarine invertebrates. The abundance of non-native species relative to native species declines significantly after extreme freshwater events. In relatively dry years, recruitment is tightly linked to seasonal temperature fluctuations, while in wet years, recruitment is much more strongly correlated with salinity fluctuations. Dramatic shifts in community composition are also evident. We suggest that the ability of dominant species to withstand these salinity fluctuations can be especially important in determining the resulting community's composition and structure.