Independence Lake is home to one of only two remaining wild, self-sustaining populations of the Lahontan cutthroat trout (Oncorhynchus clarkii henshawi), listed as a threatened species under the Endangered Species Act. It has been extirpated from almost the entirety of its historic range. Other fish species include the brook trout (Salvelinus fontinalis), brown trout (Salmo trutta), kokanee salmon (Oncorhynchus nerka), and mountain whitefish (Prosopium williamsoni).
