Speciation is the result of an accumulation of reproductive barriers between populations, pinpointing these factors is often difficult. However, hybrid zones can form when these barriers are not complete, especially when lineages come into contact in intermediate or modified habitats. We examine a hybrid zone between two closely related riverine turtle species, Sternotherus depressus and S. peltifer, and use ddRAD sequencing to to understand how this hybrid zone formed and elucidate genomic patterns of reproductive isolation. First the geographic extent and timing of the hybrid zone formation is established to provide context for understanding the role of extrinsic and intrinsic reproductive isolating mechanisms in this system. Then, the strength of selection on taxon-specific contributions to maintenance of the hybrid zone is inferred using a Bayesian genomic cline model. These analyses find a role for selection inhibiting introgression in some genomic regions at one end of the hybrid zone and promoting introgression in many loci at the other. When selective pressures necessary to generate outliers to the genomic cline are considered with the geographic and temporal context of this hybrid zone we conclude that habitat-specific selection likely limits introgression from S. depressus to S. peltifer in the direction of river flow. However, selection is mediating rapid, unidirectional introgression from S. peltifer to S. depressus which is likely facilitated by anthropogenic habitat alteration. These findings indicate a potentially imminent threat of population-level genomic extinction for an already imperiled species due to ongoing human-caused habitat alteration.