I conducted an inventory of freshwater fishes throughout the Aleutian Archipelago and examined mercury (Hg) concentrations in threespine stickleback (Gasterosteus aculeatus) collected at formerly used defense (FUDs) sites at Adak Island. I investigated fluctuating asymmetry of threespine stickleback traits from populations collected at FUDs and reference sites. Seven species of freshwater fishes were documented at 13 islands and fishes were documented in 70% of lakes trapped and 76% of streams trapped. Mean Hg concentrations for stickleback ranged from 0.314 to 0.560 mg/kg dry weight and were significantly higher at lakes associated with seabird use compared to non-seabird lakes and lakes with FUDs. The δ¹³C stable isotope ratios of sticklebacks collected from seabird lakes suggest a marine input of contaminants. Few stickleback traits demonstrated fluctuating asymmetry; most traits demonstrated directional asymmetry. These results provide important baseline data for freshwater fish management and for understanding sources of Hg contamination in this region.