Species conservation requires a clear understanding of habitat availability and subsequent use of those habitats. In cases where species declines have occurred and gone undetected by conservation managers, habitat alteration, fragmentation, and loss are often the largest contributors. River fragmentation often results in altered flow regimes, subsequently impacting the availability of riverine habitats. Blue sucker (Cycleptus elongatus) is associated with riffle and run habitat, which is especially impacted when river flows are altered. The goal of this research was to identify the extent of blue sucker habitat and mobility of the species in the Colorado River, Texas. To understand habitat selection and use, blue suckers (N = 49) were surgically implanted with telemetry tags. During 2015–2017, thirty-eight attempts were completed to relocate individuals. Optimized hotspot analysis identified three river reaches critical for blue suckers that accounted for 20% of the study area. Blue suckers used these locations year-round including during spawning. Habitats used by blue sucker were composed of gravel, cobble, boulder, and bedrock typically in riffle and run habitat. Mobility, as measured by home range size, increased as riffle density decreased. Larger home ranges were presumably necessary to find habitat to complete aspects of their life history. Results of this study suggest suitable habitats are limited throughout the fragmented riverscape. Conservation action in the form of habitat construction or increased stream connectivity through barrier mitigation could have positive impacts on the future of blue suckers in the lower Colorado River, Texas.