In 1991, the San Juan River Seven-Year Research Program was initiated. Subsequently, in 1992, the Research Program was placed under the auspices of the San Juan River Basin Recovery Implementation Program (SJRIP). The Research Program involved a variety of activities designed to characterize the status of the resident fish community (particularly the federally-protected Colorado pikeminnow Ptychocheilus lucius and razorback sucker Xyrauchen texanus); to identify and quantify those factors (biotic and abiotic) that may be limiting protected fish species, as well as other native fish species; and to identify management and conservation activities that may contribute to recovery of protected species. Much of the research begun under the Seven-Year Research Program has been completed and a variety of management and conservation activities initiated. The SJRIP drafted the Long Range Implementation Plan to guide and provide a means of evaluating progress towards achieving species recovery. It was designed to provide for “adaptive management” wherein research and particularly management or conservation activities were modified to reflect new information. To aid in the practice of adaptive management, the Long Range Plan identified monitoring of the San Juan River native and nonnative fish populations as a necessary components to “evaluate management actions and to document the [SJRIP’s] progress toward achieving species recovery” (Element 4). The monitoring protocols detailed herein were developed from methodologies used during the Seven-Year Research effort and subsequent modifications as developed and accepted by the SJRIP. These methods were based upon published literature, the professional experience of each researcher, peer discussions and review, and project evaluations. The SJRIP Monitoring Plan and Protocols was initially implemented in 1999 based on protocols developed for specific life stages and abiotic factors (Propst et al. 2000). The monitoring protocols contained herein are the third revision to the Monitoring Plan and Protocols (2009 Monitoring Plan and Protocols Workshop). To aid in the evaluation of achievement of these SJRIP goals, the following Monitoring Plan and Protocols’ goals were developed (see Recipient/Reclamation Involvement Below).