Many once coupled habitats are now disconnected due to human infrastructure that prevents not only the transfer of organisms but also fundamental ecosystem processes. Here we investigate the importance of hydrologic connectivity between remnant floodplain and freshwater intertidal marsh habitats for zooplankton metacommunity dynamics and juvenile Chinook salmon growth in the Sacramento-San Joaquin Delta, California, U.S.A. during a connected flood and disconnected drought year. Hydrological connection led to highly similar zooplankton communities between habitats. Further, we found that connected intertidal marsh habitats had approximately twice the total abundance of zooplankton of upstream floodplains and, in some cases, 15 times greater abundance than during disconnection. Gut content analysis demonstrated that salmon in our study utilized these abundant zooplankton food resources which likely contributed to elevated juvenile salmon growth rates in connected intertidal marsh habitats, where salmon had 25% greater growth rates (mm day-1) than those reared in disconnected marsh habitats. These results provide strong evidence for the importance of connectivity for metacommunity dynamics as well as productivity in historically coupled ecosystems and provide important information for future management and restoration.