Our objective was to evaluate the status of lake trout Salvelinus namaycush rehabilitation in South Bay, Lake Huron. Standardized surveys were conducted to quantify natural recruitment, annual mortality, and the contribution of wild- versus hatchery-origin lake trout. Some indicators suggest a high level of natural recruitment. The spawning population was comprised of multiple ages, and the mean age of spawners (8.4 years for females, 7.9 years for males) was at least 1 year older than the age at 50% maturity (5.8 years). Estimated annual total mortality rates (0.20–0.25) and sea-lamprey induced mortality rates (0.02) were less than maximum allowable values. The proportion of wild-origin fish captured was high among spawners but varied among sampling programs (42% in fall trap nets, 70% in fall gill nets, and 88% in summer gill nets). A strong year class (1997) could be tracked from 2001 to 2005. Few fish were captured from early (< 1996) or later (1999–2002) year classes. Possible explanations for low natural recruitment during these later years include declining spawning habitat quality caused by low water levels and/or invasion of non-native mussels (Dreissena spp.) and/or direct or indirect effects of alewife (Alosa pseudoharengus).