Abstract We investigated the effects of geothermally influenced waters on the distribution of rainbow trout, Oncorhynchus mykiss, and brown trout, Salmo trutta, in the Firehole River and its tributaries in Yellowstone National Park (WY, USA) from June 1997 to June 1998. Geothermal features in the Firehole River basin elevate mineral content and temperature in portions of the river and its tributaries. We found concentrations of boron and arsenic to be elevated in geothermally influenced areas compared with upstream sites. Boron concentrations occasionally exceeded 1,000 μg/L, a proposed limit for the protection of aquatic organisms. Arsenic concentrations occasionally exceeded 190 μg/L, the chronic ambient water quality criterion. Temperatures in geothermally influenced sites ranged up to 30°C and were consistently 5 to 10°C higher than upstream sites unaffected by geothermal inputs. Rainbow trout occurred at sites with elevated concentrations of boron, arsenic, and other trace elements and elevated water temperatures. Rainbow trout inhabited and spawned at sites with the most elevated trace element concentrations and temperatures; however, brown trout were absent from these sites. Water temperature may be the major factor determining brown trout distributions, but we cannot exclude the possibility that brown trout are more sensitive than rainbow trout to boron, arsenic, or other trace elements. Further investigations are needed to determine species-specific tolerances of boron, arsenic, and other trace elements among salmonids.