Recharge is considered a key parameter in groundwater models for sustainable management of aquifers, which is influenced by factors such as land use, soil and weather. The present study was conducted to couple WetSpass-M and MODFLOW models in the Neyshabur–Rokh Basin. To this aim, the simulated recharge by the WetSpass-M model was applied as an input into MODFLOW to assess the groundwater balance. The hydrodynamic coefficients were determined by calibrating the model, and the model sensitivity to the hydraulic conductivity coefficient, specific yield and recharge was evaluated. The results indicated that the annual average of surface runoff, actual evapotranspiration, interception and recharge during 1991–2017 equalled 18, 36, 7.6 and 42.6% of the average annual precipitation in the basin, respectively. The accurate alignment of simulated and observed water levels, along with the achievement of suitable evaluation criteria values in both steady and transient states, demonstrates the WetSpass-M model’s precision in estimating recharge and successfully integrating the two models. The groundwater balance assessment revealed a significant deficit in the aquifer, with the model demonstrating greater sensitivity to the hydraulic conductivity coefficient and providing valuable insights for the sustainable management of the Neyshabur aquifer.