The objectives of this research were to examine some representative surface waters in the Yazoo River Basin (YRB) during the growing season for a few selected herbicides; to compare the type and abundance of pesticides in the atmosphere at a agricultural and an urban site; to determine the load of nitrogen and phosphorus being discharged from the YRB to the Mississippi River and ultimately the Gulf of Mexico; to determine how the adsorptive properties of a common Delta soil differ under no-tillage (NT) versus conventional tillage (CT) for two commonly used herbicides; and to validate the Soil and Water Assessment Tool (SWAT) model for herbicide runoff in the YRB. Herbicides, in low concentrations (generally less than 10 parts per billion) were frequently detected in 3 streams in the YRB throughout the growing season. Pesticides were detected in air and rain samples from both urban and agricultural areas. The concentrations in the agricultural area generally were an order of magnitude higher and types of pesticides detected were different: more insecticides in the urban area and more herbicides in the agricultural area. The annual load of nitrogen being contributed to the Mississippi River from the YRB was less than what might be expected based on discharge, and the load of phosphorus was slightly higher than what might be expected. The amount of atrazine and fluometuron adsorbed was similar for a soil under CT and NT, but much more herbicide was adsorbed by the NT soil. At the scale of the Bogue Phalia Basin (too large for specific information to be available and too small for averaging to eliminate the need for site specific data) there are considerable uncertainties associated with input data and these, together with the simplifying assumptions within the model, mean that SWAT should not be used to predict the exact date, time, and concentration of a pesticide in a stream. However, the model does offer the potential to assess the likelihood of contamination of surface waters by a given compound in a given situation and as such could provide a useful tool for planning, management and regulatory purposes.