But with development of the Tahoe Keys, the Upper Truckee River was channeled to the lake and currently the streamflow of the two tributaries combine only during high runoff.

Two large sphagnum bogs, Grass Lake and Osgood Swamp are located in the watershed and both are considered to be Significant Natural Areas by the California Department of Fish and Game (CDFG).

The reach of the Upper Truckee above Christmas Valley is under study for inclusion in the federal Wild and Scenic Rivers system.

Threatened native Lahontan cutthroat trout (Oncorhynchus clarki henshawi) have been reintroduced into the river in the Meiss Meadows area, and the endangered shorezone plant Lake Tahoe yellowcress (Rorippa subumbellata) is found near the mouth of the river on the shores of Lake Tahoe.

Spills of treated wastewater from the South Tahoe Public Utility District's export facilities in this watershed are an ongoing concern.