Groundwater is a primary source of drinking water; however, groundwater depletion constitutes a common phenomenon worldwide. The present research aims to quantify groundwater depletion in three aquifers in Greece, including the porous aquifers in the Eastern Thermaikos Gulf, Mouriki, and the Marathonas basin. The hypothesis is to reverse the phenomenon by adopting an environmentally acceptable methodology. The core of the suggested methodology was the simulation of groundwater using MODFLOW-NWT and the application of managed aquifer recharge (MAR) by using water from small dams after the generation of hydropower. Surface run-off and groundwater recharge values were obtained from the ArcSWAT simulation. The predicted future climatic data were obtained from the Coordinated Regional Climate Downscaling Experiment (CORDEX), considering the Representative Concentration Pathway (RCP) 4.5 and the climate model REMO2009. Groundwater flow simulations from 2010 to 2020 determined the existing status of the aquifers. The simulation was extended to the year 2030 to forecast the groundwater regime. In all three sites, groundwater depletion occurred in 2020, while the phenomenon will be exacerbated in 2030, as depicted in the GIS maps. During 2020, the depletion zones extended 11%, 28%, and 23% of the aquifers in Mouriki, the Eastern Thermaikos Gulf, and the Marathonas basin, respectively. During 2030, the depletion zones will increase to 50%, 42%, and 44% of the aquifers in Mouriki, the Eastern Thermaikos Gulf, and the Marathonas basin, respectively. The simulation was extended to 2040 by applying MAR with the water from the existing dams as well as from additional dams. In all sites, the application of MAR contributed to the reversal of groundwater depletion, with a significant amount of hydropower generated. Until 2040, the application of MAR will reduce the depletion zones to 0.5%, 9%, and 12% of the aquifers in Mouriki, the Eastern Thermaikos Gulf, and the Marathonas basin, respectively. Apart from over-pumping, climatic factors such as long periods of drought have exacerbated groundwater depletion. The transformation of dams to mini-scale hydropower facilities combined with MAR will benefit clean energy production, save CO2 emissions, and lead to an economically feasible strategy against groundwater depletion.