Freshwater systems across North America and Eurasia are home to inconspicuous species of fish known as sculpins (genus Cottus). As generally small, benthic species, sculpins have largely been ignored by humans. One lineage in particular, Cottopsis, is endemic to the west coast of North America and inhabits diverse geographic areas and ecological conditions. Such complexity is the perfect setting for understanding issues related to speciation, divergence, population structure, gene flow, and phylogeography of freshwater fishes. Comprehensive phylogenetic work using multiple nuclear and mitochondrial markers generated species trees and delimitations which varied slightly by technique and statistical approach, but which revealed a number of cryptic lineages and relationships within the clade. Three species groups in particular showed remarkable variation in California, riffle (C. gulosus) and Pit (C. pitensis) sculpin, and prickly sculpin (C. asper). Following an extensive distributional sampling, a number of phylogeographic breaks, cryptic lineages, and speciation mechanisms were discovered. Within C. gulosus and C. pitensis, the Sacramento River proved to be distinctive showing potential historical hybridization, complete C. pitensis mitochondrial introgression, and restricted contemporary population structure. Consistent with other studies, a phylogeographic break along the Sacramento/San Joaquin River Delta led to the prospective divergence of C. pitensis into the Sacramento/Pit River basin and C. gulosus into the San Joaquin River basin; with different measures of isolation by distance and intra-population structure. A similar break and population structure was seen in inland C. asper populations. Estimated to have diverged from amphidromous coastal populations 110,000 years ago, inland C. asper represent incipient speciation, as evident by poor phylogenetic distinctiveness. Low measures of gene flow and hybridization in the narrow connective corridor between coastal and inland populations, along with no sign of physical barriers suggest inland C. asper are diverging by way of parapatric speciation. A novel lineage of C. asper in Clear Lake is also well-supported, originating from coastal, not inland populations. Overall, results clearly signify sculpin are a complex species group, with structure reflective of their historical hydrology, and worthy of intensive conservation and management strategies.