The distribution and relative abundance of Westslope Cutthroat Trout (WCT) Oncorhynchus clarkii lewisi in relation to habitat characteristics remain unknown across large portions of the species’ range. The goals of this research were to provide a foundational understanding of WCT distribution and relative abundance related to habitat characteristics in tributaries of the St. Maries River, Idaho—a highly altered watershed. The basin drains an area of approximately 1,863 km² and has a longitudinal elevation difference of about 207 m. Backpack electrofishing and habitat assessments were conducted at 68 reaches in 35 different tributaries of the St. Maries River in 2017 and 2018. Habitat was measured at small (reach-level) and large (watershed-level) scales. A total of 652 WCT was sampled from 52 of 68 total reaches. Habitat characteristics varied by age-class, but most WCT were estimated to be age 0 and age 1. Logistic regression models indicated that the presence of age-0 WCT was positively related to stream gradient and elevation, but negatively related to water temperature, road density, fine substrate, stream depth, and the presence of Brook Trout (BKT) Salvelinus fontinalis. The relative abundance of age-0 WCT was positively associated with road density and inversely related to wetted width, canopy cover, and elevation. The presence of age-1 and older (age-1+) WCT was positively related to gradient, canopy cover, and elevation, but negatively associated with road density, temperature, stream depth, and the presence of BKT. Relative abundance of age-1+WCT was positively associated with gradient, large substrate, canopy cover, and road density. Conversely, the relative abundance of age-1+WCT was inversely related to wetted width and elevation. This research indicates that WCT populations can persist in response to altered landscapes when suitable habitat exists. However, unmitigated threats, such as nonnative species competition (e.g., BKT), hybridization with Rainbow Trout O. mykiss, habitat loss, and habitat fragmentation, pose persistent complications to WCT abundance in locations where populations appear robust but their actual abundance is unknown.