Butterfly assemblages were studied from 2004 to 2007 at sites along the San Diego River. The purpose was to provide baseline information in the face of possible river improvement projects. We sampled in a protected area and in urban environments in hopes of identifying butterfly assemblages associated with a variety of riparian types. Multivariate analysis identified environmental variables significantly associated with butterfly assemblages such as riparian rank, soil moisture, air temperature, wind speed, nectar abundance, and forb & graminoid richness. There were significant correlations between butterfly species richness, butterfly abundance and a variety of environmental variables, including % shade. Sites located in the Mission Trails Regional Park contained unique butterfly species and were considered high value reference sites. Some butterflies of conservation interest were encountered such as: Panoquina errans Skinner, 1892 (Hesperiidae), Zerene eurydice Boisduval, 1855 (Pieridae), Tharsalea hermes W.H. Edwards, 1870 (Lycaenidae), and Apodemia virgulti Behr, 1865 (Riodinidae). A butterfly-centric metric was derived using species richness and significant variables identified via multivariate analysis to aid in management/monitoring of San Diego riparian sites.