This study examines the effect of pumping, hydrogeology, and pesticide characteristics on pesticide concentrations in production wells using a reactive transport model in two conceptual hydrogeologic systems; a layered aquifer with and without a stream present. The pumping rate can significantly affect the pesticide breakthrough time and maximum concentration at the well. The effect of the pumping rate on the pesticide concentration depends on the hydrogeology of the aquifer; in a layered aquifer, a high pumping rate resulted in a considerably different breakthrough than a low pumping rate, while in an aquifer with a stream the effect of the pumping rate was insignificant. Pesticide application history and properties have also a great impact on the effect of the pumping rate on the concentration at the well. The findings of the study show that variable pumping rates can generate temporal variability in the concentration at the well, which helps understanding the results of groundwater monitoring programs. The results are used to provide guidance on the design of pumping and regulatory changes for the long-term supply of safe groundwater. The fate of selected pesticides is examined, for example, if the application of bentazone in a region with a layered aquifer stops today, the concentration at the well can continue to increase for 20 years if a low pumping rate is applied. This study concludes that because of the rapid response of the pesticide concentration at the drinking water well due to changes in pumping, wellhead management is important for managing pesticide concentrations.