San Diego has 11 hydrologic units (watersheds) that drain into the Pacific Ocean including: Carlsbad, Otay, Penasquitos, Pueblo, San Diego, San Dieguito, San Juan, San Luis Rey, Santa Margarita, Sweetwater, and Tijuana. A watershed includes important fish and wildlife, habitat, and important natural filtering resources for the ecosystems they support. In San Diego, these watersheds have shared many of the same water quality concerns such as decline in surface water quality and habitat degradation. Some of the major stressors are associated with urban and agricultural runoff. Biological monitoring of streams and rivers is a crucial process in protecting the biological integrity of waters. "Bioassessment" (biological assessment) is used to evaluate the biological condition of a body of water using biological monitoring and other direct measurements of resident biota in surface waters. Evaluating the benthic macroinvertebrate (BMI) community of a body of water is a useful way to assess aquatic health. The BMI communities are found everywhere, and are sensitive to anthropogenic pollutants and other stressors. They can provide a great amount of information on the biological condition and health of an aquatic system. In Southern California the SoCal Benthic Index of Biotic Integrity is used (B-IBI) to assess stream health. The San Diego Regional Water Quality Control Board in efforts with the San Diego Stormwater Monitoring Coalition provided taxonomic data and B-IBI scores from 1996-2012 for this study. The San Diego Coastkeeper, a non-governmental organization, also provided valuable information for two years, 2011 and 2012. The focus of the study was to analyze this bioassessment data to assess the biological condition of these San Diego County watersheds, to determine the stressors that affect watershed health, and to evaluate temporal tends and spatial relationships in the data. The biological condition of the San Diego Hydrologic Region was assessed using BIBI scores for five hydrologic units; Carlsbad, San Diego, San Dieguito, San Luis Rey, and Sweetwater. The five hydrologic units were found to be impaired. The upper region of only one hydrologic unit (San Luis Rey) and only a single site (site 904ECEFxx) along Escondido Creek showed improvement in B-IBI scores as a function of time. Percent of developed land uses in the drainage area of sites was not found to be a significant factor affecting B-IBI scores. However, sites in the lower regions of watersheds were in poorer condition as compared to the upper regions of these same watersheds. The distance of sites to the coast was also significantly correlated to B-IBI scores. Seasonal variation was found to not affect stream health. Monitoring stream health with the collection of bioassessment remains an important part of protecting and restoring the waters of San Diego County.