This study compared traditional community analysis with stable-isotope trophic analysis to define process-based trophic elements of community structure in the eastern Gulf of Mexico, and developed a predictive capability regarding changes to fish community structure that would be expected from increasing eutrophication. Specifically, it used an existing trawl survey program (SEAMAP) to compare invertebrate herbivore (sponge and sea urchin) isotopes with groundfish isotopes, and then compared the resulting spatial patterns with spatial variation in community structure, as identified by cluster analysis. The comparison was applied to seven NMFS survey zones that extended offshore from the Caloosahatchee River, FL northwest to Mobile Bay, AL. Isotopic patterns were consistent with the presence of an oligotrophic-eutrophic spatial gradient in this region. δ15N values increased in the northwestward direction in herbivores and in each of the 17 fish species examined. In the southern NMFS survey zones, δ13C was elevated in shallow depths for individual fish species, but not in herbivores, indicating a higher proportion of benthically derived biomass contributed to the biomass of fish in the shallow parts of the southern NMFS zones. Fish community analysis using SIMPROF created a similar pattern, with distinct nearshore and offshore communities and also a northwesterly community transition. Among the 17 fish species, five appeared to have obligate dependence on either benthic or planktonic basal resources, while twelve species appeared to be have facultative relationships. Impairment of current water-quality (nutrients, turbidity, light transmission, chlorophyll a) is expected to lead to reductions in the abundance of both obligate and facultative benthic-dependent fishes.