Rainier's many lakes originally contained no fish, but had thriving populations of amphibians including salamanders. The rivers were inhabited by migratory trout and salmon, which have been greatly affected by the construction of dams further downstream that now block every major drainage.

Between 1915 and 1972 the Park Service repeatedly stocked at least 25 different Rainier lakes with trout, to improve angling opportunities. As many as 9 million fry were released, at first using pack horses, then aircraft where a five-gallon plastic bag full of fish would be poured out while flying over a lake. Using just two years as an example, Mystic, Chenuis, Green, Green Park, Bench, Marsh, Snow, and Three Lakes were stocked in 1960, then Adelaide, Eleanor, George, Hidden, James, Marjorie, Oliver, and Palisades Lakes in 1961. The new fish included non-native species (brook trout, sockeye salmon) plus native species such as cutthroat and rainbow/steelhead trout that were introduced to areas they did not historically occupy.

It is strange how blind the park was to preserving aquatic habitat for so many years. Long after the management policy for mammals, birds, and trees shifted from "make it the most fun for visitors" to "preserve in natural state", nobody batted an eye at releasing all these fish. The first proper biological study of a Rainier lake didn't occur until 1966, at Mowich Lake, and only in 1993 did a study identify presence of the rare native bull trout, which is now a threatened species.

Non-native fish compete with and may also prey on native fish and amphibians. Current fishing regulations require catch-and-release for native species, but encourage eating or euthanization of any non-native fish that may be caught.