Historically, 23 freshwater mussel species have been documented from the Buffalo National River (BNR), a 246 km, free-flowing river in northern Arkansas. The potential threats to BNR include land use/land cover changes, eutrophication, recreation, physical habitat changes, and various climate change-related effects. Twelve quantitative mussel bed sites were established and then sampled using a stratified random sampling protocol to evaluate the long-term changes between 2006 and 2020–2021 in population and assemblage characteristics. We compared (1) overall mussel bed persistence, sampling confidence levels and study-wide relative abundances, and compared species’ size and size-frequency distributions; (2) 10 overall site assemblage variables using paired t-tests; (3) site-level mean density, richness, and diversity indices using pair-wise Mann–Whitney U statistics; and (4) assemblage composition using Non-Metric Multidimensional Scaling. The major findings included the following: (1) sampling efforts based on a targeted 80% confidence level appears relatively robust, (2) BNR mussel assemblage composition and structure were relatively stable (however, small mussel bed persistence is a concern), (3) 7 of 23 sites were outliers based on freshwater mussel composition and habitat characteristics, and (4) assemblage composition changed with three species declining (Actinonaias ligamentina, Lasmigona costata, and Ptychobranchus occidentalis) and four species increasing (Cambarunio hesperus, Cyclonaias tuberculata, Eurynia dilatata, and Venustaconcha pleasii) between monitoring events.