Although habitat alteration and degradation in riverine systems are the major threats to overall mussel assemblages to date, no or few studies have been able to document significant differences in habitat variables between species. The purpose of this study was to evaluate microhabitat associations of three federally threatened freshwater mussel species, Fusconaia burkei (Walker, 1922) (Tapered Pigtoe), Hamiota australis (Simpson, 1900) (Southern Sandshell), and Pleurobema strodeanum (Wright, 1898) (Fuzzy Pigtoe), and a common mussel species, Elliptio pullata (Lea, 1856) (Gulf Spike), at 3 localities in the Choctawhatchee River watershed in southeast Alabama and northwest Florida. Depth, current velocity, and compaction were measured, and a sediment core sample was collected for each individual mussel encountered. The Kruskal-Wallis H-test was performed to determine differences in each variable measured and each sediment size class among the mussel species at each site, followed by the Mann-Whitney U-test after applying Bonferroni's correction if significant. Six out of nine times, current velocity (3 times), depth (twice), and compaction (once) were significantly higher for the threatened species compared to E. pullata, whereas there were no differences in these variables between a set of any two threatened species within a site. This study suggests that E. pullata was associated with shallow and slow flowing water and loose sediment (usually stream banks), while the threatened species used deeper and relatively faster flowing water with more compact sediment. Anthropogenic disturbances are causing Coastal Plain streams to become more sand-bottomed and shallower, which is suited to species such as E. pullata and/or its host fishes, while the species in this study preferring deeper and faster flowing water and more compact sediments are in decline.