A previously developed steady state three-dimensional groundwater flow (MODFLOW-2005) and advective transport (MODPATH6) model was used to examine subsurface nitrate transport to wells and receiving streams in two subcatchments contributing to the Upper Chester River, Maryland. Multiple scenarios of flow and transport parameter fields (recharge, hydraulic conductivity, and porosity) were previously calibrated against groundwater levels, stream discharge measurements, and atmospheric tracer measurements, as described in https://doi.org/10.1016/j.jhydrol.2018.02.006; those multiple scenarios are also available as a USGS data release (https://doi.org/10.5066/F7SN087R). Two of the flow and transport scenarios calibrated in Zell et al. (2018) were selected to simulate nitrate transport, with MODPATH6 files updated as necessary to represent advective transport from observation wells with subsurface nitrate measurements. The development of the model input and output files included in this data release and the application of the models to nitrate transport simulation are documented in the Journal of Environmental Quality article (https://doi.org/10.2134/jeq2018.11.0408).