To elucidate relationships between land cover and water quality along the central California coast, we collected monthly samples from 14 coastal waterway outlets representing various degrees of human development. Sites were distributed between three salinity categories, freshwater, estuarine, and marine, to better understand land cover-water quality relationships across a range of coastal aquatic ecosystems. Samples were analyzed for fecal indicator bacteria (FIB), dissolved nutrients, stable nitrogen isotopes in particulate organic matter, and chlorophylla (chla). Sediment samples from 11 sites were analyzed for the concentration of the anthropogenic organic contaminant perfluorooctane sulfonate and its precursors (ΣPFOS). While the data indicated impairment by nutrient, microbial, and organic contaminants at both agricultural and urban sites, the percentage of agricultural land cover was the most robust indicator of impairment, showing significant correlations (p<0.05) to FIB, nutrient, chla, and ΣPFOS levels. FIB densities were strongly influenced by salinity and were highest at sites dominated by agriculture and urbanization. Nutrient levels and chla correlated to both agricultural and urban land use metrics as well. Positive correlations among FIB, nutrients, chla, and ΣPFOS suggest a synergy between microbial, nutrient, and organic pollution. The results emphasize the importance of land management in protecting coastal water bodies and human health, and identify nutrient, microbial, and organic pollution as prevalent problems in coastal California water bodies.