<p>Historic landscape-scale geological change often shapes contemporary distributions and phylogeographic patterns of species. Because of the long count of geologic events like glaciations, colonization or vicariance often yields distinct genetic signals. For species of conservation concern, understanding these processes can be an important part of identifying potential threats, addressing questions related to recolonization or potential sources of genetically similar populations for restocking after extirpations. Here, we assess the genetic variation and demographic history of the Illinois state–listed mottled sculpin (<i>Cottus bairdii</i>) which is found in four basins across northern and eastern Illinois (Rock, Fox, Des Plaines, and Vermilion Rivers). We reveal both geological and anthropogenic factors have shaped contemporary population structure of the species. Geologically, glaciated versus unglaciated regions better explain the biogeographical patterns of distribution compared to river distance between distant watersheds across Illinois. Within the glaciated region, phylogeographic patterns suggest northward post-Pleistocene colonization. Anthropogenically, our landscape genomic analyses limited to the Illinois River basin identify dams as significant barriers to gene flow and further quantify that each dam is the equivalent of 2.7&#xa0;km of river. Additionally, each basin shows a unique demographic signal with two of the three basins showing recent population declines, one of which is associated with range contraction observed over the past century. As such, management efforts should consider three separate Evolutionary Significant Units of <i>C. bairdii</i> as they further implement conservation measures.</p>