Expansion of an invasive Lake Trout Salvelinus namaycush population in Swan Lake, Montana, threatens a core area population of Bull Trout S. confluentus. Given the recent development of novel suppression methods, such as use of carcass analog pellets to cause high mortality of embryos, there was a need to quantify spawning season aggregation sites, site use, and spawning habitat for Lake Trout in Swan Lake. Acoustic tags were implanted in 85 Lake Trout during the summer in 2018 and 2019. Nightly tracking efforts during autumn in both years resulted in 1,744 relocations for 49 individual Lake Trout. Kernel density analysis was used to evaluate Lake Trout aggregation sites, identifying 10 distinct sites. All spawning sites were located in the littoral zone along areas of steep bathymetric relief, and these sites composed 48% of total relocations during both spawning seasons. In 2019, side-scan sonar imaging was used to classify and quantify the total area of spawning substrate, which constituted 12.8% of the total surface area estimated for spawning sites 1, 6, and 9 and 11.4% of the total surface area for aggregation sites 2–5, 7, 8, and 10. Simultaneous treatment of all spawning sites would require 205,709 ± 86 kg of carcass analog pellet material, resulting in 370.4 ± 0.2 kg of phosphorus inputs and 7,487.9 ± 3.1 kg of nitrogen inputs to Swan Lake. Thus, pellet treatment would increase the Carlson's trophic state index (TSI) values from 20.8 to 27.7 for total phosphorus and from 22.1 to 26.2 for total nitrogen. Based on a TSI threshold of less than 40 for an oligotrophic lake, the use of carcass analog pellets could be feasible for supplementing the gill-netting suppression of Lake Trout in Swan Lake.