Following completion of the San Juan River Seven Year Research Program in 1997, the need to monitor San Juan River fish assemblages was recognized by the San Juan River Recovery Implementation Program Biology Committee. Autumn sampling of large- and small-bodied fishes was conducted in 1998 following procedures used during the Seven Year Research Program. In 1999, autumn sampling of fish assemblages followed procedures detailed in the draft San Juan River Monitoring Plan and Protocols. Beginning in 2000, autumn fish assemblage monitoring followed the protocols detailed in the San Juan River Monitoring Plan and Protocols (Propst et al. 2000).