Fishing at Eagle Lake, California
Eagle Lake is the only watershed which supports native Eagle Lake trout (Oncorhynchus mykiss aquilarum). These rainbow trout grow to very large sizes, possibly having evolved to live longer as low flows often restrict spawning runs up their main spawning stream, Pine Creek. The average size of Eagle Lake trout are about 1.5 pounds and can exceed 10 pounds. Adults quickly grow to a size of 17 to 18 inches in three years and can live for up to 11 years. Since these Modoc Lakes are high in alkalinity, the trout have evolved to be the only known trout subspecies capable of surviving in the alkaline waters of Eagle Lake. Eagle Lake Rainbow descendants, however, are planted with high success in many other lakes in California. These trout were once so abundant that there was a commercial fishery for them in the late 19th century. At the same time, extensive logging and heavy livestock grazing caused Pine Creek to change from a permanent to an intermittent stream in its lower reaches. In the early 1950s the few remaining eagle lake rainbow trout at the mouth of Pine Creek were rescued and used to start a hatchery program to maintain the species and the sport fishery.

Because of the complete dependence of Eagle Lake rainbow trout on hatchery production, the American Fisheries Society considers it to be a threatened species and NatureServe has listed it as critically imperiled. Peter Moyle considers it to be one of the most endangered salmonids in California. However, a petition for listing the Eagle Lake rainbow trout as a threatened species was rejected by the U.S. Fish and Wildlife Service in 1994, and a similar petition was rejected by the California State Fish and Game Commission in 2004. From 2007 to 2009 Bogard Spring Creek, a tributary to Pine Creek, was electrofished to remove non-native brook trout (Salvelinus fontinalis).

Non-native fish have not survived in the lake because of its high alkalinity, although in the early 1900s during a period of higher lake levels and falling alkalinity, Largemouth bass (Micropterus salmoides) and Brown bullhead (Ameiurus nebulosus) became abundant in the lake for some years.
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