Habitat occupancy patterns of lake trout (Salvelinus namaycush) and lake whitefish (Coregonus clupeaformis) in two large Canadian Shield lakes were modelled based on detections of fish from repeated depth‐stratified surveys over several summers. Lake trout and lake whitefish consistently occupied sites outside traditional thermal envelopes and were not detected at some sites within these ranges. This included the metalimnion and shallow epilimnion for lake trout and lake whitefish in Lake Opeongo. Physical habitat covariates were not important in defining lake trout habitat in both lakes. Physical habitat as represented by the hardness/softness gradient based on acoustic substrate surveys was important for lake whitefish in Lake Opeongo but not in Smoke Lake. In addition, thermal envelopes for lake whitefish differed between the lakes possibly because of differences in substrate slope. The wash zone of lakes, where the thermocline contacts the substrate, appears to be a physical habitat feature for lake whitefish in some lakes. Lake whitefish also exhibited diurnal activity behaviour that was reflected through greater detection rates in the morning versus the afternoon. By accounting for imperfect detection, true estimated overall occupancy of lake trout and lake whitefish increased 0.15–0.30 over naïve occupancy. Thermal habitat envelopes for lake trout and lake whitefish are wider than previously thought. Lake trout occupied a consistent thermal habitat envelope while lake whitefish varied between lakes likely because of lake specific differences in basin morphology and wash zone.