AbstractLarge, Coastal Plain rivers of the southeastern United States contain some of the most diverse freshwater communities in North America; however, surveying the fauna of these large rivers presents numerous logistical and statistical challenges. We assessed the contemporary distribution, abundance, and habitat associations of the endangered fat threeridge mussel Amblema neislerii throughout the Apalachicola River system in northwestern Florida. To achieve this goal, we used side scan sonar to map the distribution of mesohabitats and conducted a system-wide, quantitative survey to define mussel habitat associations. We then used habitat and mussel data to develop predictive models of spatial distribution and to estimate the abundance of fat threeridge across the entire Apalachicola River system. Findings revealed a broadly distributed (i.e., 128 river kilometers occupied), robust population of approximately 9 million individuals (95% CI = 5–12 million), with a center of distribution (i.e., where abundance and occurrence were highest) approximately 45–80 river kilometers upstream of the river mouth. Fat threeridge primarily occupy fine sediment mesohabitats characterized by smooth/plane bedforms that are clearly definable via sonar habitat mapping. We hypothesize that this species may be particularly sensitive to the availability of stable, fine sediments during one or more critical life history phases and that the availability of this habitat may explain its restricted distribution in tributary rivers. Our study provides a quantitative, replicable foundation upon which future population and habitat monitoring can be based.