Sandelia bainsiiis a range‐restricted and highly threatened freshwater fish endemic to South Africa. Recent genetic evidence suggests that this species comprises three allopatrically distributed lineages that have been informally designated asSandeliasp. “Kowie,”Sandeliasp. “Keiskamma” andSandeliasp. “Buffalo.” As these lineages have only been recently identified and are likely to face a high risk of extinction because of restricted distributions, there is a critical need for generating ecological information to guide conservation prioritisation. The present study compared the historical and current distribution patterns, together with the habitat associations ofSandeliasp. “Kowie” in the Koonap and Kat rivers, tributaries of the Great Fish River. This study indicated that this lineage has been extirpated from one of the three localities in the Koonap River where it was historically abundant. In the Kat River, the current distribution ofSandeliasp. “Kowie” was comparable to its historical range, but its future persistence is threatened by the presence of non‐native piscivores, instream physical barriers and potential future exploration for shale gas and infrastructure development in the Karoo Basin. A generalised hurdle negative binomial model revealed that although this lineage's probability of occurrence was high in habitats with boulder and sand substrates, and low conductivity, habitat characteristics were poor predictors of its abundance. Thus, it was postulated that the current range of this lineage probably represents the only available habitats for the persistence of different life stages for this taxon. Alternatively, the observed patterns may suggest the possibility of a shift in habitat associations, possibly for optimum utilisation of the remaining refugia within this river system. Immediate conservation measures should focus on preventing the spread on non‐native invasive fishes, whereas future studies should evaluate the impacts of population fragmentation and identify appropriate intervention measures to maintain this lineage's long‐term adaptive potential.