This study aims at modeling groundwater flow using MODFLOW in a transboundary hardrock–alluvium aquifer, located in northwestern Oman. A three-dimensional stratigraphic model of the study area representing the vertical and spatial extent of four principal hydro-geologic units (specifically, the Hawasina, ophiolite, Tertiary and alluvium) was generated using data collected from hundreds drilled borehole logs. Layer elevations and materials for four layers grid cells were taken from the generated stratigraphic model in which the materials and elevations were inherited from the stratigraphic model that encompasses the cell. This process led to accurate grid so that the developed groundwater conceptual model was mapped to simulate the groundwater flow and to estimate groundwater balance components and sustainable groundwater extraction for the October 1996 to September 2013 period. Results show that the long-term lateral groundwater flux ranging from 4.23 to 11.69 Mm³/year, with an average of 5.67 Mm³/year, drains from the fractured eastern ophiolite mountains into the alluvial zone. Moreover, the long-term regional groundwater sustainable groundwater extraction is 18.09 Mm³/year for 17 years, while it is, respectively, estimated as 14.51, 16.31, and 36.00 Mm³/year for dry, normal, and wet climate periods based on standardized precipitation index (SPI) climate condition. Considering a total difference in groundwater levels between eastern and western points of the study area on the order of 228 m and a 12-year monthly calibration period (October 1996 to September 2008), a root mean squared error (RMSE) in predicted groundwater elevation of 2.71 m is considered reasonable for the study area characterized by remarkable geological and hydrogeological diversity. A quantitative assessment of the groundwater balance components and particularly sustainable groundwater extraction for the different hydrological period would help decision makers to better understand the water resources in the Al-Buraimi region. In addition, it would assist decision makers to improve existing strategies to enhance the decision making for future developments.