Kuyui- refers to the Cui-ui, a species of fish endemic to Pyramid Lake which is central to the lives of the Northern Paiute band called the Kuyui Dükadü (cui-ui-fish-eaters).

[14] In the Lower Watershed, Steamboat Creek, which drains Washoe Lake, is the major tributary to the Truckee River.

Beavers were re-introduced to the Truckee River watershed and Tahoe Basin by the California Department of Fish and Game (CDFG) and the U. S. Forest Service between 1934 and 1949 in order to prevent stream degradation and to promote wetland restoration.

[19] Supporting this line of evidence, Tappe records in 1941 an eyewitness who said beaver were plentiful on the eastern slope of the Sierra Nevada on the upper part of the Carson River and its tributaries in Alpine County until 1892 when they fell victim to heavy trapping.

[22] The presence of beaver dams has been shown to either increase the number of fish, their size, or both, in a study of brook, rainbow and brown trout in nearby Sagehen Creek, which flows into the Little Truckee River at an altitude of 5,800 feet (1,800 m) and is a stream typical of the eastern slope of the northern Sierra Nevada.

[23] Not only have aspen and cottonwood survived ongoing beaver colonization but a recent study of ten Tahoe streams utilizing aerial multispectral videography, including Trout Creek and Cold Creek, has shown that deciduous, thick and thin herbaceous vegetation has increased near beaver dams, whereas coniferous trees are decreased.

[24] Benefits of beaver dams include removal of sediment and excessive pollutants travelling downstream, which improves water clarity, which was shown to worsen when beaver dams were recently removed in nearby Taylor Creek and Ward Creek.

Starting from the outlet gates at Lake Tahoe stretching about 3 miles (4.8 km), the run ends at the River Ranch Restaurant.

[27] The Truckee also boasts a healthy, self-sustaining non-native Brown trout (Salmo trutta) population.

Under the direction of the U.S. Environmental Protection Agency, a comprehensive dynamic hydrology transport model was developed by Earth Metrics Inc.[28] The model's name was subsequently changed to DSSAM, and it was applied to analyze land use, and wastewater management decisions throughout the Truckee River Basin of 3,120 square miles (8,081 km2) and to provide guidance in other U.S. river basins.

Based on the use of the model, some decisions have been influenced to enhance riverine quality and aid the viability of associated biota.

It is thought that dumping raw sewage into the Truckee River is a detriment to the water quality in several communities.