The Mobile Basin has undergone extensive channel modification with corresponding declines in the distribution and abundance of native aquatic fauna. However, many of the declining aquatic species of the Mobile Basin may persist within unmodified sub-basins. The Noxubee River is a sub-basin of the Mobile Basin that is relatively unaltered throughout its watershed, and we hypothesized that the system could serve as a refugium for declining riverine species of the Mobile Basin. We characterized species richness and assemblage structure of fishes in the Noxubee River and its tributaries to determine whether or not contemporary fish assemblages resembled the historical assemblages as described before construction of the Tennessee-Tombigbee Waterway. We found that fish assemblages of the contemporary river are similar to those of the historical river, and many species now absent from another portion of the Mobile Basin are still present and maintain similar distribution and abundance patterns. Our results are informative because there is little existing information available regarding fish assemblages in the Noxubee River since major alterations were imposed upon the Mobile Basin through construction of the waterway. These results are discussed relative to findings from another Mobile Basin tributary that exhibited a marked change in many fish assemblage properties following construction of the waterway. Variable resiliency among tributaries to altered main-channel rivers illustrates the need for predictive tools that can be employed to prioritize conservation efforts.