The seasonal habitat use of Salvelinus fontinalis (Brook Trout) and sub-yearling Salmo salar (Atlantic Salmon) was examined in Hart Brook, a tributary of Lake Ontario. Fish habitat use and available habitat were examined during summer and autumn. Interspecific differences in habitat use occurred as well as intraspecific seasonal differences. Overyearling Brook Trout were more selective in their habitat preferences than subyearling Brook Trout or juvenile Atlantic Salmon. Depth and the amount of cover were significantly different among the three fish groups. Salmon occupied faster and shallower water than either age group of trout. Atlantic Salmon were also associated with larger-sized substrate materials than either trout age group, and salmon occurred in habitats with less cover than trout. Overyearling Brook Trout occupied deeper water with more cover than subyearling trout. All three salmonid groups occupied areas with more cover in autumn compared to summer. In autumn, subyearling Brook Trout used deeper areas than they had in the summer. In Hart Brook, the habitat of subyearling Atlantic Salmon can be generally characterized as riffles, the habitat of overyearling Brook Trout was deep pools with extensive cover (35%), and that of subyearling trout was any area with moderate flow and at least 20% cover. As efforts proceed to reintroduce Atlantic Salmon in Lake Ontario, further research is needed to ensure the conservation of Brook Trout populations.