Most fish in Yosemite National Park have been introduced. Prior to trout stocking for sport fishing, native fish were limited in both range and number of species (see species list ). The series of glaciations that covered much of the area that is now the park eliminated all fish from the high country. After the glaciers retreated, the waterfalls and steep gradients that were created on the rivers and streams by glaciation prevented repopulation of fish by upstream migration. Only the lower reaches of the Tuolumne and Merced Rivers were populated by fish when Euro-Americans first arrived in Yosemite in the mid-1800s.
Because of severe climatic conditions, low nutrient availability associated with snowmelt over granitic watersheds, and a lack of spawning habitat, fish introduced in many of Yosemite's lakes have not survived. Fish surveys conducted in 1977 at 102 lakes that have a history of fish planting found that about 55% of these lakes contained self-sustaining fish populations, while 22% of the surveyed lakes had reverted to a natural, fish-free state, and another 24% were expected to achieve this state. A re-survey of some of these lakes in 1996, however, found a number of the lakes expected to go fishless still contained fish. It is estimated that approximately 550 miles of streams in Yosemite support fish. The rainbow trout is the only trout native to Yosemite, and was originally restricted to the Merced River in Yosemite Valley and downstream. Widespread planting of rainbow trout, brown trout, and brook trout has introduced these fishes to many waters in the park that were naturally fish-free, causing adverse effects to aquatic ecosystems.
Beginning in 1978, a park policy was implemented that, by 1991, ended almost 100 years of fish stocking in Yosemite. This policy recognized that non-native fish were having an adverse effect on native aquatic ecosystems that had evolved in the absence of fish. Predation by non-native fish is identified as one of the primary reasons for the precipitous decline of mountain yellow-legged frogs ( Rana muscosa ) in the Sierra Nevada, including Yosemite. This species is currently under consideration by the U.S. Fish and Wildlife Service for listing as endangered. Non-native fish have also likely had profound effects on aquatic invertebrate communities. Scientists from the Sierra Nevada Aquatic Research Lab (SNARL) surveyed over 3,000 lakes and ponds in 2000 and 2001 evaluated fish, amphibian, and invertebrate populations to shed more light on the possible effects of non-native fish. The data from this research is currently being analyzed.
Introduction of non-native strains of rainbow trout have probably affected the genetic integrity of the native rainbow trout found in the lower reaches of the Merced River (including Yosemite Valley) and the Tuolumne River.