An integrated technique of Gravity Recovery and Climate Experiment (GRACE) data along with other data-sets to estimate the variations of groundwater storage over Libya and its zones. Temporal (January 2003–December 2015) terrestrial water solutions (ΔTWS) of GRACE with outputs of Global Land Data Assimilation System (GLDAS) model were used. Findings are: (1) the Western Libya (zone 1), Eastern Libya (zone 2), and Northeastern Libya (zone 3) areas are receiving an average annual precipitation of 48, 30, and 154 mm/ yr, respectively, (2) the average GRACE-estimated groundwater storage variations (ΔGWS) were −4.13 ± 0.47 mm/yr, −3.36 ± 0.44, and +0.25 ± 0.14 mm/yr; however, the average annual extraction rates of −4.96 ± 0.50 mm/yr (−3.08 ± 0.31 km3/yr), −2.22 ± 0.22 mm/yr (−1.9 ± 0.19 km3/yr), and −0.31 ± 0.03 mm/yr (−0.042 ± 0.004 km3/yr) were from zones 1, 2, and 3, respectively, (3) the observed depletion in groundwater of zones 1, and 2 is largely related to the prevailed dry conditions over these zones and the heavy anthropogenic effects, (4) the minor recharge of 0.83 ± 0.69 mm/yr (0.52 ± 0.43 km3/yr) is happening over zone 1 from the surrounding highlands and from the rainfall over the northern coastal areas, and is compensating for part of the groundwater withdrawal, (5) the groundwater in zone 2 is partially flowing northeastward to the Dakhla basin along the preferred groundwater flow conduit of the Pelusium megashear system, and partially flowing northward to the Mediterranean Sea, (6) zone 3 is receiving a minor recharge of 0.56 ± 0.14 mm/yr (0.077 ± 0.02 km3/yr), and (7) a progressive increase in Cl-36 groundwater ages supports the groundwater flow directions along structures that are sub-parallel to the flow direction. The integrated technique provides a practical and informative study.