Pesticide applications to agricultural lands in California, USA, are reported to a central data base, while data on water and sediment quality are collected by a number of monitoring programs. Data from both sources are geo-referenced, allowing spatial analysis of relationships between pesticide application rates and the chemical and biological condition of water bodies. This study collected data from 12 watersheds, selected to represent a range of pesticide usage. Water quality parameters were measured during six surveys of stream sites receiving runoff from the selected watershed areas. This study had three objectives: to evaluate the usefulness of pesticide application data in selecting regional monitoring sites, to provide information for generating and testing hypotheses about pesticide fate and effects, and to determine whether in-stream nitrate concentration was a useful surrogate indicator for regional monitoring of toxic substances. Significant correlations were observed between pesticide application rates and in-stream pesticide concentrations (p < 0.05) and toxicity (p < 0.10). In-stream nitrate concentrations were not significantly correlated with either the amount of pesticides applied, in-stream pesticide concentrations, or in-stream toxicity (all p > 0.30). Neither total watershed area nor the area in which pesticide usage was reported correlated significantly with the amount of pesticides applied, in-stream pesticide concentrations, or in-stream toxicity (all p > 0.14). In-stream pesticide concentrations and effects were more closely related to the intensity of pesticide use than to the area under cultivation.