The Leon River, a small-medium river in central Texas, is highly impacted by multiple impoundments, enrichment from agricultural runoff, and decreased dissolved oxygen levels. This degraded river contains sixteen unionid species, two of which are both endemic to the region and candidates for the federal endangered species listing (Quadrula houstonensis and Truncilla macrodon). While there is a short historical record for this river basin and a recent modern survey completed in 2011, zooarchaeological data adds evidence for conservation efforts by increasing the time depth of data available and providing another conservation baseline. Zooarchaeological data for the Leon River is available from the two Late Holocene archaeological sites: 41HM61 and the Belton Lake Assemblages. Data generated from these assemblages describe the prehistoric freshwater mussel community of the Leon River in terms of taxonomic composition and structure. By comparing this zooarchaeological data to the data generated by the longitudinal modern survey of the Leon River, long term changes within the freshwater mussel community can be detected. A conceptual model is constructed to evaluate how robusticity, identifiability, and life history ecology affect unionid taxonomic abundances in zooarchaeological data. This conceptual model functions as an interpretive tool for zooarchaeologists to evaluate forms of equifinality in zooarchaeological assemblages. This thesis determines differences between the late Holocene and modern freshwater community of the Leon River, explores how different alternative mechanisms influence zooarchaeological data, and exemplifies of how zooarchaeological data can be used for conservation biology.