Water resources management is a vital need in arid and semi-arid regions such as Sinai Peninsula, Egypt. Accordingly, the sustainability of water resources in this arid environment should be examined in terms of the possibility of groundwater recharge, particularly through runoff water, while identifying the most appropriate potential sites for drilling new water wells to cover current and future needs. The aquifer system of El-Qaa Plain in South Sinai is considered one of the structural basins associated with the tectonic setting of the Gulf of Suez. It is the main source of high-quality water in South Sinai. The present work provided an integration of mathematical flow modeling, hydrochemical composition, environmental isotopic signature, watershed modeling system (WMS), and remote sensing (RS) tools to determine the aquifer sustainability and recharge mechanisms. The obtained results indicated the following: (a) the salinity of the water ranged between 326.4 and 2261 ppm, while the environmental isotope values ranged between −6.28 to −4.48‰ for δ18O and −29.87 to −21.7‰ for δ2H, which reveals the phase of recharge and mixing between ancient water and recent rainwater; (b) sites for three dams in three sub-watersheds were proposed to harvest approximately 790,000 m3/y of runoff water to enhance groundwater recharge of the aquifer system; (c) and five scenarios using MODFLOW indicated that water drawdown is acceptable by adding 10 new production wells (discharge rate increased by 3600 m3/day). Moreover, increasing the recharge rate by 2% from the base case, leads to an increase in the piezometric water level with an average value of 0.13 masl, which reflects the positive effects of the proposed runoff water harvesting facilities. The integration applied in this work represents an integrated management system for water resources (surface and groundwater) which is suitable for application in arid or semi-arid coastal and similar areas.