Human impacts continue to alter community structure, emphasizing the need to understand how spatial and temporal variability in disturbance and conservation affect ecological communities to optimize management strategies. Here, we quantify fish species richness, diversity, and community structure across five coastal bays and lakes in the Lavaca–Colorado Estuary, Texas, over 30 years to investigate spatial and temporal variability in species assemblages, and the potential effects of resource management. Results suggest that fish communities varied both spatially and temporally from 1976 to 2008, with greater temporal shifts in habitats more proximate to the Gulf of Mexico and removed from human residential areas — diversity increased in Powderhorn Lake and spotted seatrout (Cynoscion nebulosus (Cuvier, 1830)) and red drum (Sciaenops ocellatus (L., 1766)) abundances increased in Oyster Lake following changes in fishing regulations. Natural fluctuations in environmental conditions coupled with limited access to lakes by geographic restraints may have led to more pronounced changes in community structure. However, the effects of fishing management on fish communities within small lakes and bays within the Lavaca–Colorado Estuary is likely habitat- and context-specific, and continued monitoring, especially among ecologically and economically important species, will provide insight into how environmental change and anthropogenic disturbance may affect long-term trends in coastal community composition.