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In this study, bioassessment data collected between 1998 and 2005 were synthesized and analyzed for streams and rivers throughout the San Diego Hydrologic Region to provide a spatial and temporal context for the results of several monitoring projects conducted between 1998 and 2005 and to ascertain the applicability of the Southern California benthic macroinvertebrate index of biological integrity (SoCal B-IBI) to the region's streams. The water quality of the sites studied in the region, as reflected by temporal and spatial analyses of SoCal B-IBI scores, was found to be quite poor. When streams were analyzed individually most showed stable scores over the time frame of the study with some showing better scores in the fall. Spatially, scores were found to be better farther away from the coast in the upstream reaches of the watersheds. This study further explored the applicability of the SoCal B-IBI to a focused geographic region by demonstrating the necessity of each component metric to the assignment of biological condition. Although all component metric scores were deemed to be necessary, the percent intolerant individuals score had a more significant effect in driving impairment. The analysis of the component metrics of the SoCal B-IBI provides useful insights to the changes in scores among and between the sampled sites in the region's watersheds. Based on this study, natural resource management agencies responsible for managing water quality should incorporate regular measures of biological integrity into their water quality programs to ascertain regional and temporal trends. DOI: 10.1061/(ASCE)EE.1943-7870.0000193 CE Database subject headings: Biological processes; Watershed management; Assessment; Water quality; California. Author keywords: Bioassessment; Biological integrity; Watershed assessment; Biocriteria.