Shoepack Lake in Voyageurs National Park, Minnesota, supports a genetically unique population of muskellunge. Over a two-year period, we collected population data using multiple mark-recapture methods and exploitation data from angler surveys. Additional fieldwork yielded data on age structure, growth, age of maturity and fecundity. We estimated the initial adult population size to be 1120 fish (95% confidence interval - 842-1399). Angler surveys revealed catch rates averaging 0.262 fish per angler per hour. Anglers harvested few fish in part because only 4% of captured fish were above the 762 mm minimum length. Natural mortality was estimated as 0.0451. Female growth rates were <50 mm a year with little or no growth beyond 722 mm. Male growth rates were <50 mm a year with little or no growth beyond 663 mm. Growth rates, ultimate lengths, and condition were lower than reported for lakes in Ontario and Wisconsin. Rain-induced washout of a large beaver dam reduced the surface area of Shoepack Lake by roughly one-half during our study, providing dramatic evidence for potential future environmental changes. We estimated the ratio of effective population size (N[subscript e]) to absolute population size (N) using demographic data. We generated a set of potential scenarios based on our data, literature values and reasonable assumptions about angler exploitation, environmental conditions and carrying capacity. We then simulated the effects of each scenario on future population size using Fisheries Analysis and Simulation Tools (FAST) for 100 years, and used our calculated N[subscript e] to N ratio to estimate simulated N[subscript e] in each simulation year. Simulated N[subscript e] ranged from 165-855. Scenarios yielded N[subscript e] ranging from completely below to completely above the "500" guideline in which populations are considered "safe" from significant erosion of genetic variation. Reduction of carrying capacity, such as would be expected to occur following surface area reductions like the one we witnessed, was the primary cause of low N[subscript e] values in our simulations. Our results suggest that both natural phenomena and future changes in exploitation could threaten the genetic variability of the muskellunge population in Shoepack Lake. We recommend Voyageurs Nation Park maximize carrying capacity and reduce angler related mortalities.