Fast water transfer to rivers during floods causes a water deficit during dry periods. For a long-term retention of water in aquifers and its subsequent use in drier or heavier demand periods, the Managed Aquifer Recharge (MAR) techniques were studied and implemented in four pilot areas of the DEEPWATER-CE project funded by the Interreg CENTRAL EUROPE programme. In Slovakia, the Recharge Dam MAR type was investigated using the groundwater numerical modelling technique in order to retain the surface water in an aquifer and to recharge the groundwater for its subsequent use for irrigation during dry periods. The calibrated and verified groundwater flow model was developed using MODFLOW and was used for the prediction of two scenarios (prognosis) improving the water level regime in the channel system of Rye Island resulting in the improvement of the groundwater regime as well. By appropriate manipulation of the gate slides during flood situation, the amount of water recharged to the groundwater can be increased by 11,000 m3.d−1 without further technical measures. After the construction of three additional weirs, the amount of water recharged to the groundwater can be even higher.