Nonpoint source fecal contamination is a concern for drinking water supplies worldwide. In this study, 4812 E. coli isolates were classified to source. Results of this experiment show that the fecal coliform (FC) counts varied by year, month, and site, for each of the watersheds sampled. For both years, the lowest FC counts tended to be at the highest elevation sites followed by the drinking water intake sites at the lowest elevation. The highest FC counts tended to be at the mid-elevation sites on BX, Deer, and Duteau Creeks. The sources of E. coli varied significantly with stream for 2003 and 2004 (P < 0.001, df = 39), although the main sources of E. coli (avian, deer/elk, canine, rodent, bovine, and bear) tended to be similar between watersheds. The dominant sources of E. coli changed from 2003 (avian, deer/elk, and canine) to 2004 (avian, bovine, and rodent). It is important to look at the results of more than 1 year of source tracking data to get a better picture of the dominant sources within a watershed. Overall, wildlife was the largest contributor of E. coli to the watersheds in both 2003 (> 84%) and 2004 (> 73%).