A survey of lakes and streams was conducted in 2004 for fish and amphibians. This survey detected nine species of fish of which five are native to parts of California. Native species include rainbow trout, tui chub, speckled dace, Lahontan redside and Tahoe sucker. Brook trout, Brown trout, golden shiner, and flathead minnow are all species that are non-native to the park that were detected during this survey.
Fish stocking occurred prior to the park being established in 1916. Most of the lakes in the park were stocked with rainbow, brown, and brook trout. It is suspected that the goldern shiner and flathead minnow were introduced as bait that was used by fishermen and escaped. Due to National Park Service policy, all stocking of fish was halted in the park and currently most of the lakes where these fish were planted are currently fishless due to lack of suitable spawning grounds.
Butte Lake, Snag Lake, and Horseshoe Lake are all popular fishing destinations in the park with populations of rainbow, brown, and brook trout. Kings Creek and Grassy Swale Creek both have populations of brook trout as well. The most popular fishing lake in the park, however, is Manzanita Lake. This lake holds a fair number of rainbow and brown trout and is rated as a blue ribbon fly fishery by the state of California Department of Fish and Game. It is managed as a catch and release fishery with only single barbless hooks allowed. No bait such as worms, salmon eggs or powerbait may be used. This lake is nationally known for its fly fishing opportunities.