The Azraq Wetland Reserve (AWR) with a 74 sq. km surface area in the eastern desert of Jordan is one of the wetlands preserved under the RAMSAR Convention since 1977. Less than 15% of the wetland area has been preserved compared to the past. The wetland is located in the center of the Azraq Basin, a transboundary basin with a semiarid climate. Pumping groundwater from the deep aquifer complexes meets most of the water demand. This study aimed to estimate groundwater fluxes and depths in and around the AWR during the recent period (2013-2020). More specifically, the model is intended to be used a) as a tool to facilitate understanding of the groundwater flow dynamics in the AWR, b) as a decision-support tool to preserve the groundwater-dependent wetland ecosystem; c) to determine critical areas of decline in groundwater levels. A regional, three-dimensional transient groundwater flow model was developed using Modelmuse 5.1.1, which is a public-domain graphical user interface of the finite-difference flow model MODFLOW-2005. The model was calibrated using the automatic parameter estimation code PEST. The measures of model fit suggest overall acceptable model errors. The simulation results appropriately represent the regional patterns of groundwater flow in the Azraq Basin and yield meaningful water balances comparable with previous studies’ findings. The modeling results provided critical information regarding groundwater level changes over the past eight years. It can be concluded that groundwater levels in the AWR are highly dependent on groundwater flow and budget components in the basin as a whole. According to the model results, the groundwater level in the AWR declined by an average of 0.83 m per year. Furthermore, the model results indicated that the groundwater depth under the AWR increased to 22m below the ground level at the end of the simulation period.