The Alabama River drainage is a biologically diverse system containing over 180 native fishes and at least 33 endemics. Many studies have surveyed single species of conservation concern, such as the federally endangered Scaphirhynchus suttkusi (Alabama Sturgeon), Alosa alabamae (Alabama Shad), and Crystallaria asprella (Crystal Darter), but few have documented entire fish assemblages. Maintaining fish-assemblage data is an important process in monitoring species and assemblage composition through time so that large-scale ecological change can be detected. In this study, we surveyed fish assemblages of sand/gravel bar habitat in the lower Alabama River and compared these data to those collected from historical surveys. Diel and seasonal surveys were conducted along 19 sandbars from Dixie Landing (river mile 22) to Claiborne Lock and Dam (river mile 72). We recorded a total of 48 species in 41 collections during summer, fall, and spring 2010–2011. Based on the Jaccard index, these samples had low similarity to historical samples collected by R.D. Suttkus and the Geological Survey of Alabama, suggesting temporal fish assemblage shifts. In 2010, we detected extremely high numbers of Brevoortia patronus (Gulf Menhaden) during summer and fall, which is a new distributional record. Diel comparisons using the Morisita index indicate low similarity reflecting large numbers of catfish species detected mostly in night collections. These data also indicate seasonal faunal changes among sandbar fish assemblages. Ongoing habitat alteration on the Alabama River is a potential factor leading to assemblage homogenization and potential loss of biodiversity. Future monitoring in the Alabama River should consider diel and seasonal sampling to accurately document fish species and assemblages, including potential shifts that may be occurring over space and time.