Brook trout are the one of the only Salvelinus species native to eastern North America and range from Canada to Georgia. Very little is known, however, about the ecology of the southern form of this species. We quantified microhabitat use of southern brook trout in Ball Creek NC, a third-order stream, during six seasonal samples (summer 2010, autumn 2010, spring 2011, summer 2011, autumn 2011 and spring 2012). In general, trout preferentially occupied deeper microhabitats with lower mean velocities and higher amounts of erosional substrata than were randomly available. Older trout (1+ and 2+) occupied deeper microhabitats with lower mean velocities than yearling trout. These microhabitats typically represent ‘plunge pools’. Southern brook trout also occupied focal point velocities that were statistically indistinguishable from optimal velocities calculated for rainbow trout in the same system and thus may chose microhabitats that maximise net energy gain. Southern brook trout are found in isolated populations, and management strategies should focus on the preservation of plunge pool habitat for conservation of this subspecies.