Stocking programs for Muskellunge Esox masquinongy throughout North America rely on the collection of wild adult Muskellunge to acquire gametes for hatchery propagation. The process of collecting, transporting, confining, handling, and spawning broodstock Muskellunge may cause mortality that could alter Muskellunge density, size structure, and population survival rates. We used long‐term Muskellunge capture–recapture data collected from the Iowa Great Lakes and Clear Lake in northern Iowa to estimate the number and proportion of Muskellunge captured annually and the initial mortality rates resulting from broodstock collection. We also evaluated whether Muskellunge apparent survival rates differed between individuals used as broodstock and those that were not captured annually. Finally, we evaluated whether the number of initial mortalities or the number of individuals captured were related to annual population survival estimates. Collectively, 7,010 adult Muskellunge (3,896 males and 3,114 females) captures occurred between 2001 and 2017, and population densities within a system ranged from 0.11 to 0.39 fish/ha. An average of 33% (range = 13–76%) of the population was captured during broodstock operations annually. Between 0 and 28 (0.0000 to 0.0191 fish/ha) Muskellunge died at each hatchery annually, and more males died than females (total of 150 males and 68 females; 3.9% and 2.2% of captured fish, respectively). However, annual mortalities were generally a low proportion of Muskellunge in the lake (<2%; <0.001 fish/ha). There was some evidence of size‐selective mortality, particularly for males, where larger individuals (875–975 mm) were more likely to die, but we found no evidence to suggest that broodstock collection affected annual population survival estimates. Muskellunge broodstock mortality appears to act in a compensatory manner with natural mortality, and other sources of population mortality are more likely to have a greater effect on the population.