Elevated levels of nitrate (NO3) in surface water and groundwater can degrade water quality and also pose serious threats to human health in drinking water. In this study, the Soil Water and Assessment Tool (SWAT) is linked with the finite difference groundwater flow model MODFLOW and a groundwater solute reactive transport model RT3D (Reactive Transport in 3 Dimensions) to provide a systemic understanding and representation of the complex network of interactions between the land surface, subsurface, and surface water systems.