The positioning of fishes within a riverscape is dependent on the proximity of complementary habitats. In this study, foraging and non-foraging habitat were quantified monthly over an entire year for a rainbow trout (Oncorhynchus mykiss) population in an isolated, headwater stream in southcentral New Mexico. The stream follows a seasonal thermal and hydrologic pattern typical for a Southwestern stream and was deemed suitable for re-introduction of the native and close relative, Rio Grande cutthroat trout (O. clarkii virginalis). However, uncertainty associated with limited habitat needed to be resolved if repatriation of the native fish was to be successful. Habitat was evaluated using resource selection functions with a mechanistic drift-foraging model to explain trout distributions. Macroinvertebrate drift was strongly season- and temperature-dependent (lower in winter and spring, higher in summer and fall). Models identified stream depth as the most limiting factor for habitat selection across seasons and size-classes. Additionally, positions closer to cover were selected during the winter by smaller size-classes (0, 1, 2), while net energy intake was important during the spring for most size-classes (0, 1, 2, 3). Drift-foraging models identified that 81% of observed trout selected positions that could meet maintenance levels throughout the year. Moreover, 40% of selected habitats could sustain maximum growth. Stream positions occupied by rainbow trout were more energetically profitable than random sites regardless of season or size-class. Larger size-classes (3, 4+) were energetically more limited throughout the year than were smaller size-classes. This research suggests that habitat in the form of deep pools is of paramount importance for rainbow trout or native cutthroat trout.