Increasing water demands, especially in arid and semi-arid regions, continuously exacerbate groundwater resources as the only reliable water resources in these regions. Groundwater numerical modeling can be considered as an effective tool for sustainable management of limited available groundwater. This study aims to model the Birjand aquifer using GMS: MODFLOW groundwater flow modeling software to monitor the groundwater status in the Birjand region. Due to the lack of the reliable required data to run the model, the obtained data from the Regional Water Company of South Khorasan (RWCSK) are controlled using some published reports. To get practical results, the aquifer boundary conditions are improved in the established conceptual method by applying real/field conditions. To calibrate the model parameters, including the hydraulic conductivity, a semi-transient approach is applied by using the observed data of seven years. For model performance evaluation, mean error (ME), mean absolute error (MAE), and root mean square error (RMSE) are calculated. The results of the model are in good agreement with the observed data and therefore, the model can be used for studying the water level changes in the aquifer. In addition, the results can assist water authorities for more accurate and sustainable planning and management of groundwater resources in the Birjand region.