The importance of main‐stem rivers and major tributaries to endangered Colorado River fishes is well documented, but the use and significance of small tributary streams remains poorly understood. Historically, these fishes probably used smaller tributaries for spawning, rearing, feeding, and refuge. Currently, the proliferation of nonnative species and altered flows may have affected tributary use by endangered fishes. In February 2008 and 2009, we installed a PIT‐tag passive interrogation array (PIA) in the San Rafael River, Utah, approximately 2 km upstream from the confluence with the Green River, and another PIA approximately 60 km upstream from the Green River confluence. Using passive detections and active captures in the San Rafael River from 2008 to 2010, we detected 15 Colorado Pikeminnow Ptychocheilus lucius, 16 Bonytails Gila elegans, 20 Razorback Suckers Xyrauchen texanus, and five “undocumented” fish. Several endangered fishes were detected on multiple occasions and across years, often moving into and out of the San Rafael River from distances up to 360 km away (range, 6–360 km). Our findings demonstrate the use and the potential importance of small tributaries and their fragile habitats to endangered fishes. Received May 13, 2012; accepted March 10, 2013

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