The principal objective of the Santee Water Quality Project is to identify hotspots of water contamination in Santee and determine if these hotspots change over time. To this aim, researchers in the Environmental Hydrology class at San Diego State University pursued existing water quality data and accessed digital elevation models and land use shapefiles to evaluate spatial and temporal patterns in water quality in Santee. The researchers were divided into four groups: bacteria, nutrient, urban trash, and hydrology. The data analyzed by the bacteria, nutrient, and trash groups consisted of spreadsheets documenting, from 2003 to 2014, water quality at different locations in Santee. The water sampling was conducted by D-Max Engineering, Inc., a San Diego–based environmental consulting firm specializing in storm water services. The hydrology group found that the alteration of streamflow is positively linked with land use change, the spread of urbanization, and the increase in impervious surfaces. Baseflows, peak flows, and flood magnitudes have steadily increased while precipitation levels have remained within the bounds of natural variation. The bacteria group found that concentrations of total coliform, fecal coliform, and enterococci were significantly higher than the permissible limits set in place by the California Regional Water Quality Control Board. Further research should follow regarding the sources of the bacteria and mitigating practices should be considered in an effort to reduce the delivery of the bacteria to the waterways. The nutrient group found that concentrations of ammonia, phosphate, and nitrate, were high during the sampling period. The concentration levels should be of concern and mitigating the effects should be a priority. The group recommends limiting access to the river by increasing restrictive measures and maintaining the existing infrastructure that prohibits access to the river.