Headwaters was established as an ecological reserve to preserve the last remaining unprotected stand of old growth redwood forest and the flora and fauna that inhabit it.
There are 3 wildlife species inhabiting the Reserve that are a candidate for listing or listed as threatened under the Endangered Species Act. The threatened species are the marbled murrelet and the northern spotted owl and candidate for listing is the Pacific fisher.
There are two federally threatened fish populations that inhabit the South Fork of the Elk River within Headwaters. These are coho salmon and steelhead trout. Chinook salmon also inhabit the South Fork of the Elk River. Salmon Creek, on the south end of Headwaters, contains resident cutthroat trout.