The North Africa region is seeking water resources to develop agricultural expansions and land reclamation projects based on the groundwater resources. Monthly (April 2002–July 2016) terrestrial water storage (TWS) solutions of the Gravity Recovery and Climate Experiment (GRACE) along with other datasets were used to monitor and estimate the variations in groundwater storage over the Sudanese area and its sections. Results indicate: (1) the Sudanese area, Southern Sudan and Northern Sudan sections are receiving an average recharge of +4.15 ± 1.07, +2.46 ± 1.69, and +4.74 ± 0.76 mm/yr, respectively during the analysed period, taking into an account the annual extraction rate of 0.67 ± 0.067, 1.04 ± 0.104 and 0.54 ± 0.054 mm/yr from the Sudanese area, Southern Sudan and Northern Sudan sections, respectively, (2) and the average groundwater storage variations of +3.35 ± 1.07, +1.21 ± 1.69 and +4.09 ± 0.76 mm/yr from the Sudanese area, Southern Sudan and Northern Sudan sections, respectively, and (3) the assumed natural discharge of −0.13 ± 0.013, −0.21 ± 0.021, and −0.11 ± 0.011 mm/yr from the Sudanese area, Southern Sudan and Northern Sudan sections, respectively. (4) The average precipitation of Tropical Rainfall Measuring Mission data over the Sudanese area, Southern Sudan and Northern Sudan sections was estimated at 520.2, 1165.6 and 300.3 km3/yr, respectively. (5) The ground surface relief is forming northeastward streams taking the surface water away to the river. (6) The groundwater flows to the southernmost part of Egypt is impeded by the Uweinat-Aswan basement uplift and the thinned sedimentary cover in northern Sudan and southern Egypt, which in turn flows northeastward to the river. (7) The integrated study is informative and cost-effective model for best estimating the recharge rate of large areas.