In this report, a restoration and monitoring plan for the San Rafael River, a tributary to the Green River in the upper Colorado River Basin, is presented. The plan is intended to guide restoration and management of the San Rafael River over the next 40-50 years and is developed as an adaptive management plan. The recommended restoration actions are intended to recover and enhance natural river processes, and are based on the best available information regarding the history of hydrologic, geomorphic, and ecological changes that have occurred on the river over the last century. Sites for implementation are prioritized systematically using data on stream and riparian habitat and potential response of native fish populations to restoration. An experimental design is recommended for implementing restoration actions. Combined with sufficient monitoring, the experimental design will help in identifying the most successful restoration actions. The most successful restoration actions can then be applied to other sites on the San Rafael River and restoration of other river systems.