Climate change in desert areas and semi-arid watersheds may offer a promising solution for the water scarcity problem that Bedouins and local inhabitants face. This study investigated the integrated water resources management in arid and semi-arid regions using rainwater harvesting in combination with the managed aquifer recharge (RWH-MAR) technique. The study also used recharge wells and storage dams to achieve the sustainability of groundwater supplies in the context of climate change and management of the flow to the Gulf of Suez. Therefore, different return periods of 10, 25, 50, and 100 years were considered for the annual flood volume resulting from those watersheds. Moreover, hydrologic modeling was carried out for the El Qaa plain area, South Sinai, Egypt, using the Watershed Modeling System (WMS) and the groundwater modeling of SEAWAT code. Our findings show that for different scenarios of climate change based on return periods of 10, 25, 50, and 100 years, the aquifer potentiality reached 24.3 MCM (million cubic meters) per year, 28.8 MCM, 36.7 MCM, and 49.4 MCM compared to 21.7 MCM at 2014 with storage of groundwater ranges 11.8%, 32.1%, 69%, and 127.4%, respectively. These findings have significant implications for the system of RWH-MAR and groundwater sustainability in El Qaa Plain, South Sinai. The RWH-MAR proved to be an effective approach that can be applied in different water-stressed and arid regions to support freshwater resources for sustainable future development and food security, as well as protect communities from extreme flash flood events.