Regulation of the Upper Tombigbee River and its incorporation into the Tennessee-Tombigbee Waterway has resulted in main-channel flows that differ from the pre-regulation condition. Flows differ in (1) magnitude: higher base flows, damped peak flows, and (2) variability: the river rises and falls faster and the number of reversals has increased. A shift in the trophic ecology of the resident fish assemblage corresponded with the altered hydrology. Assemblage-level trophic plasticity manifested through dietary shifts in species present during both time periods are coupled with changes to the taxonomic structure observed previously. Species representing the contemporary assemblage feed on fewer taxa regardless of respective trophic ecologies and include taxa that are not characteristic of diets under pre-regulation conditions. More basal resources contributing to production resulted in a greater number of trophic pathways flowing through a decreased dietary breadth. Reduced foraging efficiency is inferred for riverine specialists, possibly resulting in lower fitnesses. Tributaries are highlighted as important in maintaining biodiversity in the regulated main-channel because flows and associated trophic ecologies of resident fishes are relatively similar to those observed under pre-regulation conditions. Materials and taxa exhibit unique interactions at “zones of confluence” where unregulated tributaries merge with the main-channel. Quantifiable characteristics of trophic ecology and ecomorphology, along with connectance to free flowing major tributaries, emerge as potential indicators of the vulnerability of fishes to hydrologic alteration.