Seagrass habitats have long been known to serve as nursery habitats for juvenile fish by providing refuges from predation and areas of high forage abundance. However, comparatively less is known about other factors structuring fish communities that make extensive use of seagrass as nursery habitat. We examined both physical and biological factors that may structure the juvenile seagrass-associated fish communities across a synoptic-scale multiyear study in lower Chesapeake Bay. Across 3 years of sampling, we collected 21,153 fish from 31 species. Silver Perch Bairdiella chrysoura made up over 86% of all individuals collected. Nine additional species made up at least 1% of the fish community in the bay but were at very different abundances than historical estimates of the fish community from the early 1980s. Eight species, including Silver Perch, showed a relationship with measured gradients of temperature or salinity and Spot Leiostomus xanthurus showed a negative relationship with the presence of macroalgae. Climate change, particularly increased precipitation and runoff from frequent and intense events, has the potential to alter fish—habitat relationships in seagrass beds and other habitats and may have already altered the fish community composition. Comparisons of fish species to historical data from the 1970s, our data, and recent contemporary data in the late 2000s suggests this has occurred.