The Varaždin alluvial aquifer located in the Drava River valley. The study area is characterized by agricultural activity, which raised concerns due to the high nitrate concentration in groundwater. The present study aims to evaluate future nitrate concentrations in groundwater using the numerical groundwater flow and transport modeling. The regional model was generated in GMS software, using the MODFLOW code for steady-state groundwater flow model, and MT3DMS code for nitrate transport model. Advective-dispersive transport was simulated, without a chemical retardation process. The calibrated model was used to investigate the evolution of groundwater nitrate concentrations for the next 20 years under four scenarios: a) current nitrate input; b) zero input from wastewater; c) agricultural input reduced by 50%; d) input from natural vegetation and surface water The scenario analysis demonstrated that reducing the nitrate input from agricultural areas yields a considerable reduction of nitrate in groundwater, while the impact of wastewater is negligible. Neither of the scenarios reached concentrations below threshold value of 50 mg/L for the entire aquifer in the next 20 years. The nitrate concentration in the northern part of the aquifer will remain low, mainly due to the dilution from river. The central part of the aquifer is highly dependent on changing the on-ground nitrate concentration, showing inertia regarding the nitrate attenuation in groundwater. •The nitrate transport was simulated using advection-dispersion mechanism, without a chemical retardation.•Neither of the future scenarios reached nitrate below 50 mg/L for the entire aquifer.•Simulation results suggest agriculture as a major nitrate pollutant in the study area.