Overfishing and Sea Lamprey Petromyzon marinuspredation led to extirpation of Lake Trout Salvelinus namaycushfrom Lake Michigan in the 1950s. Large populations of hatchery‐reared fish were developed by the 1970s, but natural reproduction was limited until the early 2000s when it began to increase in the southern main basin. Hypothesizing that the relatively low mortality of spawning‐aged fish contributed to this reproductive success, we estimated the total annual mortality rate for this population. We used catch curves to estimate the total instantaneous mortality rate Zusing coded wire tags, which provided definitive ages. We made separate estimates from fish collected in three on‐going surveys: a spring gill‐net survey, a fall gill‐net spawning survey, and a sport fishery survey. Our estimates of Z± SE were 0.297 ± 0.019, 0.239 ± 0.009, and 0.205 ± 0.007 for the spring, spawning, and sport fishery surveys, respectively. We suggest that the mean Z± SE of all survey estimates of 0.247 ± 0.027 would be a reasonable estimate for this population, which equates to a total annual mortality of 22 ± 3%. This estimate is in the low range of rates reported for the species and is in the same range as other populations in the Great Lakes with well‐established natural reproduction. We concluded that these low total mortality rates contributed to the reproductive success in southern Lake Michigan through increasing spawning stock density and age structure and that previous estimates of another important population parameter, the instantaneous natural mortality rate M, were too high. Estimates of Mranged from 0.210 to 0.240 and were based on the Pauly equation, a growth‐ and temperature‐based estimator. We suggest maximum‐age‐based estimators of Mare more appropriate for Lake Trout. Several alternative maximum‐age‐based estimators produced estimates for Mof 0.132–0.058, all of which are more compatible with our estimate of Z. Impact statementFollowing a decades‐long stocking program, promising levels of naturally produced Lake Trout are emerging. We conclude that low total mortality rates contributed to the emerging natural reproduction in southern Lake Michigan through increasing spawning stock density and age structure, and that previous estimates of the background natural mortality rate were too high. This is an important finding for encouraging Lake Trout restoration elsewhere in the Great Lakes. Following a decades‐long stocking program, promising levels of naturally produced Lake Trout are emerging. We conclude that low total mortality rates contributed to the emerging natural reproduction in southern Lake Michigan through increasing spawning stock density and age structure, and that previous estimates of the background natural mortality rate were too high. This is an important finding for encouraging Lake Trout restoration elsewhere in the Great Lakes.