Brook trout (Salvelinus fontinalis) populations in the upper Shavers Fork, a high elevation watershed in eastern West Virginia, have been severely impacted by a loss of quality habitat. Successful restoration of these populations will require a comprehensive understanding of current habitat conditions at a watershed scale. We describe a statistically based habitat survey designed to quantify physical habitat conditions within the watershed at a range of spatial scales. Our study also addresses the following specific objectives: 1) to describe discrete hydraulic channel units that commonly occur in our study area, and 2) to identity statistical differences in the microhabitat characteristics among each of the channel unit types. We identified 5 recurring channel unit types within the basin: bluff pool complexes, riffle-run complexes, intermediate gradient riffles, low gradient riffles, and glides. Univariate and multivariate statistical analyses indicated that there were consistent, interpretable differences in the microhabitat characteristics of each channel unit type. Specifically, we found that channel units were most easily differentiated on the basis of variables that describe channel complexity (depth and distance to cover), stream flow (current velocity), and substrate composition. Statistically based habitat surveys, such as the one we present here, provide the basis of stream habitat management plans, and our results represent an important first step in efforts to restore a productive brook trout fishery to the upper Shavers Fork drainage.