Brook trout (Salvelinus fontinalis) habitat restoration is needed across a range of stream sizes; however, studies quantifying brook trout habitat preferences in streams of differing sizes are rare. We used radio-telemetry to quantify adult brook trout microhabitat use in a central Appalachian watershed, the upper Shavers Fork of the Cheat River in eastern West Virginia. Our objectives were to: 1) quantify non-random microhabitat use by adult brook trout in the Shavers Fork main stem (drainage area = 32 km2) and an adjacent tributary, Rocky Run (drainage area = 7 km2); and 2) construct stream-specific habitat suitability curves (HSCs) for four important microhabitat variables (depth, average current velocity, maximum current velocity within one meter, and distance to cover). Brook trout used a subset of available microhabitats in both the main stem and Rocky Run: trout tended to occupy microhabitats that were deeper, higher velocity, and closer to cover than expected by chance alone. Although specific microhabitat values differed between the main stem and tributary populations, the overall patterns in brook trout microhabitat use were consistent regardless of stream size. Habitat suitability curves were constructed based on brook trout microhabitat use and will be used to design and monitor the effectiveness of future habitat restoration efforts in the Shavers Fork watershed. Our results suggest that habitat enhancement projects that increase the availability of deep, high velocity microhabitats adjacent to cover would benefit brook trout in both small tributaries and larger river main stems.