This paper describes a two-stage system for prioritizing stream reaches and riparian communities along a given river for protection or restoration. The system uses associations between geomorphology and riparian vegetation at stream reach and community scales as a basis for defining reference conditions. First-stage reach classification involves collecting and analyzing data from topographic maps and aerial photographs. These data, along with judgment-based criteria for ranking reaches relative to reference conditions, are used to classify stream reaches as suitable for protection, recommended for mitigation or restoration within existing site-specific regulatory procedures, or requiring further analysis to evaluate community-scale restoration needs. Second-stage field sampling is conducted on the reaches needing further analysis to determine the riparian communities present, the associations between communities and floodplain landforms, and reference community conditions. This stage requires collection of field data on geomorphic conditions, plant species composition, and plant community structure. Cluster analysis or a comparable technique is used to classify plant communities associated with floodplain landforms and identify reference conditions for each landform. Community structure and species composition are compared to reference conditions to define restoration possibilities at the community scale. The combined results from stream reach and community-scale analysis provide a strategy for protecting and restoring riparian resources for a whole river. Implementation requires further site-specific information on hydrology, geomorphology, and other factors.