A two-stage system for selecting stream reaches and riparian communities for restoration was applied to the 80-km San Luis Rey River below the Lake Henshaw dam in southern California. In the first stage, data from topographic quadrangles and aerial photographs were analyzed to define and classify reaches. These analyses concluded that (1) 28 km of the river and adjacent floodplain were suitable for second-stage evaluation of restoration needs and (2) 32 km met criteria for reference conditions at the stream reach scale and should be protected from further impacts. The remaining 20 km of the river and flood-plain were considered unsuitable for restoration to reach-scale reference conditions; individual sites may be restored under existing regulatory review. Second-stage field sampling provided data on vegetation and floodplain landforms and substrate from more than 3000 plots within the 28 km of river and 1120 ha of floodplain selected for further study. Classification of floristic samples stratified by landform/substrate class indicated six primary riparian communities on the floodplain, some associated with particular flood-plain landform/substrate classes and others ubiquitous. Reference conditions for these communities were interpreted from the data. There were two major departures from reference conditions: tree-dominated communities were less extensive than historic levels and exotic plants had significantly invaded some landforms and communities, displacing natural communities. General goals would include restoration of tree communities and removal of exotics, with further consideration of site-specific objectives. The results included estimates of the areas by community type requiring restoration. The approach was developed for streams in the semi-arid western United States, but it may be adapted for use elsewhere.