Fish assemblage structure in lotic environments is a product of interactions between the habitat and the biota, but little is known about how deep pool habitat conditions affect distributional patterns of fish occupying them in larger warmwater streams. This study describes relationships between the habitat and the fish assemblages in deep pools of the Upper Tombigbee River, Mississippi. Pools exhibited an increase in size from headwaters to mouth. The change in the structure of fish assemblages was related significantly to increases in pool size while independent of time or other environmental conditions. A small amount of the variation in structure of fish assemblages in deep pools was accounted for by the measured environmental variables. This suggests other factors such as biotic interactions play an additional role in the forming the observed distributional patterns in fishes occupying deep pools.

The Mobile Basin is a prime example of a system that has undergone extensive channel modification with corresponding declines in the distribution and abundance of the native aquatic fauna. However, many of the declining aquatic species of the Mobile basin may persist within unmodified subbasins. The Noxubee River is a subbasin of the Mobile basin that has had very little alteration throughout its watershed. I investigated the species richness and assemblage structure to determine if the contemporary fish assemblage attributes resembled the conditions represented by historic collections. The findings of this study are important because the Noxubee River has not been extensively investigated since 1983, and the river could serve as refugia for declining riverine species of the Mobile basin. After examination at both local and regional levels, I determined that a diverse contemporary fish assemblage comprising 87 species, similar to historic collections, still persists in the Noxubee River system.

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.