Since 2000 there has been a major effort to raise and stock Colorado pikeminnow and razorback suckers into the San Juan River in an attempt to increase their numbers in the river and increase the probability that they can develop a self-sustaining population as required under the Recovery Goals. These propagation efforts have been accompanied by dam releases to mimic natural spring flows and extensive nonnative removal efforts in the mainstem of the river that may favor other native fishes in the system (Propst and Gido 2004). Monitoring by the San Juan River Basin Recovery Implementation Program (SJRIP) has shown a substantial increase in the numbers Colorado pikeminnow and razorback sucker captured throughout the river as well as a continued healthy population of flannelmouth and bluehead suckers (Ryden 2010). While captures of adult Colorado pikeminnow and razorback suckers are increasing, to date few juveniles are captured in river-wide surveys suggesting a potential for limited natural recruitment. Moreover, declines in roundtail chub populations indicate additional research and management may be necessary to effectively manage the entire native fish assemblage in the San Juan River basin. Study Area—The major perennial tributaries to the San Juan River are the Navajo, Piedra, Los Pinos, Animas, La Plata, and Mancos rivers, and McElmo Creek. In addition there are numerous ephemeral arroyos and washes contributing little total flow but large sediment loads. The study area will include three major tributaries of the San Juan River: McElmo Creek, the Mancos River, and Chaco Wash.