Managed aquifer recharge (MAR) is an increasingly popular technique; however, the significance of groundwater flow dynamics is rarely examined in detail regarding MAR systems. In general, a high hydraulic gradient is not favoured for MAR implementation, as it causes higher water loss and mixing of recharge water with native groundwater. However, during groundwater-dependent ecosystem (GDE) rehabilitation, these hydraulic gradient-driven flow processes can be taken advantage of. The aim of this research is to test this hypothesis by evaluating the effect of groundwater table inclination, topography, and other local characteristics on MAR efficiency from the perspective of GDE restoration. MAR efficiency was examined from recharge to discharge area in a simple half-basin based on theoretical flow simulations, using GeoStudio SEEP/W software. Different scenarios were compared to analyse the groundwater level increase and the infiltrated water volumes and to assess the efficiency of MAR based on these parameters in each scenario. The theoretical results were applied to a close-to-real situation of Lake Kondor, a GDE of the Danube-Tisza Interfluve (Hungary), which dried up in the past decades due to groundwater decline in the area. Based on the results, initial hydraulic head difference, model length, and hydraulic conductivity are the most critical parameters regarding water level increase at the discharge area. The water amount needed for increasing the water table is mainly influenced by the thickness of the unsaturated zone and the material properties of the aquifer. The findings can help better understand MAR efficiency in light of local groundwater flow processes and contribute to optimising MAR systems. The results of the study suggest that, if water is infiltrated at the local recharge area, the water table will also increase at the corresponding discharge area, which positively effects the connected GDEs. This approach can serve as a nature-based solution (NBS) to sustain sensitive ecosystems in changing climatic conditions.