The Loess Plateau of China (LPC) is suffering from the impacts of overexploitation of groundwater, leading to a decline in the regional water table. This is compounded by relatively recent large‐scale transformation of land use, which may impact groundwater recharge and threaten future water quality from intensive nitrogen fertilizer application. Understanding the regional unsaturated water flow and nitrate travel time in the deep vadose zone is crucial for the sustainable management of the LPC groundwater system. We develop here a regional‐scale model that exploits an extensive database of soil properties derived from recent intensive soil profile sampling over the LPC, together with climate, vadose zone thickness, and land use data. The model solves the Richards equation and a conservative solute transport model using a multiple 1D column approach. A comparison between model simulations and observations at five sites reveals good model performance. Application over the LPC indicates that areas with dense irrigated agricultural land use contribute significantly to groundwater recharge. By using land use cover information from 1975 to 2008, simulations reveal that the transition from agriculture to forest and grassland accounts for a small reduction of the total annual recharge (6.1%). Modeled nitrate travel times through the deep unsaturated zone range between decades and centuries; however, recent loading of anthropogenic nitrate is expected to reach the aquifer in the near future under irrigated areas or where the vadose zone is relatively thin. The model simulations provide valuable information for assessing future vulnerability of groundwater resources over a regional scale.