The Big Thicket located in Southeast Texas harbors the highest number of regional endemic freshwater mussel species and the highest diversity of unionid mussels in the state, including five state-threatened species. Unfortunately, mussels in this region are threatened by pollution, habitat alteration and destruction due to human impacts caused by petrochemical activities, climatic changes and urbanization. The goals of this project were to (1) survey mussels in the Big Thicket National Preserve, particularly in the poorly surveyed southern portion of the preserve, and (2) to examine historical changes in mussel communities. In addition, DNA samples were taken and the analysis of 97 mussels informed identification of ten species, some of which can be difficult to distinguish morphologically. A total of 39 sites in the Lower Neches River, Village Creek and Pine Island Bayou basins were surveyed. Historical data from 2002 (restricted to Village Creek) and 2014 were available for sub-set of these sites. The survey showed that species richness and mussel densities generally increased from upstream tributaries towards lower Village Creek and the mainstream Neches, where rare and threatened species were mostly found. Evidence for recruitment was mainly found in the backwaters of the lower Neches, which may act as a refuge during flooding. Declines between 2014 and 2018 were most severe in the parts of the Neches basin that most likely experienced the highest shear stress during flooding based on the channel morphology. Declines were also detected when data from 2002 were compared with 2014 suggesting that the exceptional drought in 2011 may have also contributed to long-term declines in Village Creek. Future studies should examine the role of backwaters for recruitment of threatened mussels.