<jats:title>Abstract</jats:title>
          <jats:p>Given the lack of rainfall during the dry season in Greece and other countries, groundwater is important in meeting water needs for all uses. Reliable simulation of groundwater flow and predictions of groundwater levels under different management scenarios, in light of water crisis, are essential tools for the sustainable management of aquifers. In this paper, the MODFLOW code for simulating groundwater flow was applied to the Greek section of the transboundary Serres river basin in a complex aquifer system developed in alluvial deposits. The groundwater of the basin is critical for the fulfillment of both the irrigation requirements of an extensive local agricultural activity and the domestic needs of a significant population. Data necessary for model construction and simulation was provided by the relevant authorities and literature. The model calibration is considered successful as the simulated values show a statistically acceptable fit to the measured data. Sensitivity analysis shows that the aquifer’s storage coefficient change has the greatest impact on the groundwater level. In a management scenario where groundwater extraction is reduced by 5% over a ten-year period, the groundwater level is projected to rise by approximately 0.17 m. In contrast, in the worst-case scenario, where groundwater extraction increases by 6.5% reaching at a critical point regarding the sustainability of the groundwater resources in the area, the average groundwater level is expected to drop by 0.72 m, resulting in the reduction of aquifer reserves. The model serves as a valuable tool for mitigating and adapting to the impacts of the climate crisis, as well as for formulating policies that promote the sustainable management and rational use of the aquifer.</jats:p>