The Little Choctawhatchee River watershed is currently affected by effluents from wastewater treatment plants and may be subject to impoundment as a water supply reservoir. We used historical data from the literature and the results of recent surveys (2006–2008) to assess past and current patterns of the diversity of mussels, crayfishes, and fishes throughout the river basin in order to gain information about the past and potential future effects of degraded water and habitat quality to the fauna of this region. Our results suggest that mussel assemblages have declined dramatically from historical levels, with only three of the eleven historically recorded species found. Several statelisted mussel species and candidates for federal protection formerly present are now believed extirpated from the watershed. Fish and crayfish collections during 2006–2008 were more diverse (52 and 6 species) than historical records indicated (39 and 3 species). This increased diversity was probably due to a more concentrated sampling effort in the current study than in the past. Future impoundment may cause further and possibly drastic changes to the remaining freshwater faunal diversity.