Freshwater fish surveys were conducted at 178 lakes and streams at 13 islands in the Aleutian Archipelago and two islands in the Pribilof Islands during May-September 2002 and 2006-2010. Seven fish species were documented: coho salmon (Oncorhynchus kisutch), rainbow trout (O. mykiss), Dolly Varden (Salvelinus malma), anadromous, and resident freshwater threespine stickleback (Gasterosteus aculeatus species complex), ninespine stickleback (Pungitius pungitius), coastrange sculpin (Cottus aleuticus), and Alaska blackfish (Dallia pectoralis). Resident freshwater threespine stickleback and Dolly Varden were the most commonly trapped fish. Ninespine stickleback were found only in the Near Islands group. Populations of resident freshwater threespine stickleback containing a low frequency of individuals with two or four dorsal spines were collected in the Near Islands group and at Adak Island. Sympatric species pairs of anadromous and resident freshwater threespine stickleback were collected in the Andreanof Islands, Rat Islands, and Near Islands groups. Avian piscivores were more commonly observed at lakes with fish. This study provides baseline data for freshwater fish management within the Alaska Maritime National Wildlife Refuge.