The Mississippi silverside (Menidia audens), now common throughout the Tennessee-Tombigbee Waterway (TTW) in Mississippi, apparently invaded this highly modified system from the Tennessee River, concurrent with TTW construction (1972–1985). Subsequent decline in distribution and abundance of the native brook silverside (Labidesthes sicculus) led to speculation that dietary competition with M. audens might be occurring. Therefore, diet data from sympatric and allopatric collections of the two silversides at several sites in TTW were analyzed using multivariate statistics and null models to test for significant dietary differences, overlap and niche shifts potentially attributable to habitat alteration. Diet overlap between the two silversides at sites of co-occurrence was greater than expected under the null model. Moreover, intraspecific food habits did not differ between individuals occurring in sympatry and those occurring in allopatry for either silverside. Thus, significant portions of their diet overlapped and neither species has exhibited dietary shifts that would facilitate coexistence. The two species differed significantly along stream size and current velocity gradients, with M. audens preferring the larger, slower moving habitats of the waterway. Unlike L. sicculus, M. audens included the exotic daphnid Daphnia lumholtzi in its diet. Because M. audens capitalized on a wider variety of prey items in the modified TTW environment and because of their previous interactions in other systems, we conclude that the native silverside, L. sicculus, is likely to be replaced by M. audens in lentic TTW habitats.