During July–August 2013, a gastroenteritis outbreak occurred among rafters at Idaho’s Middle Fork of the Salmon River. To identify the agent, source, and risk factors for illness, we solicited ill and well persons who rafted during July 1–September 23 to respond to an online survey, and conducted a case-control study. Cases were defined as nausea, vomiting, or diarrhea ≤25 days after rafting; control subjects were rafters who did not have these symptoms. Illness was associated with having consumed filtered river water—70% of (69/98) case subjects and 38% of (106/280) control subjects had consumed filtered water (odds ratio [OR] = 3.9; 95% confidence interval [CI] [2.4, 6.4]). In a follow-up online survey of 33 case subjects and 73 control subjects, boiling water for drinking was protective against illness; 2/18 case subjects, compared with 15/33 control subjects, had boiled their drinking water (OR = 0.2; 95% CI [0.03, 0.9]). From ill rafters, norovirus (n = 3) and Giardia (n = 8) were detected in stool specimens. Norovirus was detected on surfaces and E. coli in surface water used for drinking. Adherence to backcountry drinking water treatment recommendations is advised.