Backwards particle-tracking is widely used in groundwater modeling to gain insights into transport processes in terms of source areas, travel paths, and travel times. In this study we develop a novel modeling framework to apply this approach to SWAT-MODFLOW, a coupled surface water-groundwater model, using the particle-tracking model MODPATH. We tested the framework by applying MODPATH to a SWAT-MODFLOW model of a groundwater-dominated watershed and tracking particles backwards from a river reach with significant spring discharges to the locations where they entered the MODFLOW domain. By combining the source area information of the particles with the nitrate loading from the SWAT model, we were able to simulate nitrate concentrations in the discharged groundwater as well as to simulate changes in nitrate concentrations resulting from different land use and management scenarios. Critically, our approach developed here permits simulation of travel time distributions and source areas of water volumes and nitrate masses. We show how these source and age components can be used to guide the prioritization of water quality mitigation strategies that consider both intrinsic (i.e., hydrogeological) vulnerability as well as specific management actions that could be taken to improve surface water and groundwater quality.