Here, Lahontan cutthroats became a large (up to 1 m or 39 in) and moderately long-lived predator of chub suckers and other fish as long as 30 or 40 cm (16 in).

These trout, as well as cui-ui (Chasmistes cujus), a sucker now found only in Pyramid Lake, were dietary mainstays and were used by other tribes in the area.

During the 19th and early 20th centuries, Lahontan cutthroats were caught in tremendous numbers and shipped to towns and mining camps throughout the West; estimates have ranged as high as 1,000,000 lb (450,000 kg) annually between 1860 and 1920.

Upstream populations have been isolated and decimated by poorly managed grazing and excessive water withdrawals for irrigation, as well as by hybridization, competition, and predation by non-native salmonids.

Under the direction of the U.S. Environmental Protection Agency's comprehensive dynamic hydrology transport model, the Dynamic Stream Simulation and Assessment Model (DSSAM), was applied to analyze impacts of a variety of land use and wastewater management decisions throughout the 3,120-square-mile (8,100 km2) Truckee River Basin.

[11] These analyses allowed more competent decisions to be made regarding the watersheds, as well as the management of treated effluent discharged to the Truckee River.

[12][13] In Independence Lake, precariously low spawner numbers have recently increased along with five years of brook trout removal.

The California state record was caught in Lake Tahoe in 1911 by William Pomin, weighing 31 lb (14 kg), 8 oz (230 g).