There are several methods in California available to assess and monitor the quality of its waters. Bioassessment represents one major approach; which is the use of biological/ecological indicators (e.g. benthic macroinvertebrates) to determine the environmental quality of stream health and/or their ability to support aquatic life. Using this tool, one can determine the overall ecological health of a stream. Traditionally, bioassessments in Southern California were carried out using the SoCal Benthic Index of Biotic Integrity (SoCal B-IBI). The SoCal B-IBI does have significant limitations however; including its benchmark values being based on reference sites considered to be relatively undisturbed by human activity. Developed in 2013, a new form of bioassessment called the California Stream Condition Index (CSCI) addresses the inadequacies of the SoCal B-IBI. The CSCI combines two exceptional forms of index that have conventionally been used disjointedly: an observed-to-expected (O/E) index and a mulitmetric index (MMI). The CSCI is the first index to offer a dependable statewide standard for interpreting bioassessment data and is the foundation of the new Biological Integrity Assessment Implementation Plan statewide. The focus of the study was to analyze bioassessment data (as measured by CSCI scores) for the San Diego Hydrological Region to assess the trends in this aquatic health indicator and its relationship to chemical and physical stressors. This assessment was done using data for eight of eleven watersheds; Tijuana, San Dieguito, Santa Margarita, San Diego, San Luis Rey, Sweetwater, Carlsbad, and Peñasquitos. Between 2007 and 2015, CSCI scores for all eight watersheds (combined) were found to show significantly increased bioassessment scores (p <0.01), this reflecting the increasing ecological health of the region’s watersheds. For 2007 through 2015, CSCI scores for all watersheds in the San Diego Hydrological Region (combined) were significantly correlated (p <0.05) with levels (log transformed) of conductivity, total suspended solids, chloride, and total nitrogen and total phosphorus. Such associations between these chemical and physical stressors and the biotic quality of the San Diego Hydrologic Region will bolster the scientific underpinning of the Regional Water Quality Control Board’s efforts to regulate these pollutants and support the TMDL process for these stressors.