The Soil and Water Assessment Tool (SWAT) was used to assess the impact of climate change on sediment, nitrate, phosphorus and pesticide (diazinon and chlorpyrifos) runoff in the San Joaquin watershed in California. This study used modeling techniques that include variations of CO(2), temperature, and precipitation to quantify these responses. Precipitation had a greater impact on agricultural runoff compared to changes in either CO(2) concentration or temperature. Increase of precipitation by +/-10% and +/-20% generally changed agricultural runoff proportionally. Solely increasing CO(2) concentration resulted in an increase in nitrate, phosphorus, and chlorpyrifos yield by 4.2, 7.8, and 6.4%, respectively, and a decrease in sediment and diazinon yield by 6.3 and 5.3%, respectively, in comparison to the present-day reference scenario. Only increasing temperature reduced yields of all agricultural runoff components. The results suggest that agricultural runoff in the San Joaquin watershed is sensitive to precipitation, temperature, and CO(2) concentration changes.