Sympatric populations of native Brook Trout Salvelinus fontinalis and naturalized Brown Trout Salmo trutta exist throughout the eastern USA. An understanding of habitat use by sympatric populations is of importance for fisheries management agencies because of the close association between habitat and population dynamics. Moreover, habitat use by stream‐dwelling salmonids may be further complicated by several factors, including the potential for fish to display scale‐dependent habitat use. Discrete‐choice models were used to (1) evaluate fall and early winter daytime habitat use by sympatric Brook Trout and Brown Trout populations based on available residual pool habitat within a stream network and (2) assess the sensitivity of inferred habitat use to changes in the spatial scale of the assumed available habitat. Trout exhibited an overall preference for pool habitats over nonpool habitats; however, the use of pools was nonlinear over time. Brook Trout displayed a greater preference for deep residual pool habitats than for shallow pool and nonpool habitats, whereas Brown Trout selected for all pool habitat categories similarly. Habitat use by both species was found to be scale dependent. At the smallest spatial scale (50 m), habitat use was primarily related to the time of year and fish weight. However, at larger spatial scales (250 and 450 m), habitat use varied over time according to the study stream in which a fish was located. Scale‐dependent relationships in seasonal habitat use by Brook Trout and Brown Trout highlight the importance of considering scale when attempting to make inferences about habitat use; fisheries managers may want to consider identifying the appropriate spatial scale when devising actions to restore and protect Brook Trout populations and their habitats.Received December 11, 2015; accepted March 2, 2016 Published online June 29, 2016