Protected horticultural complexes would increase crop productivity but would adversely affect the groundwater recharge function in the area because the impervious area would increase. Further, they would limit the movement of living beings, affecting biodiversity. Therefore, this study evaluated the groundwater ecosystem services provided by protected horticultural complexes in terms of consistent utilization of water. The estimated amounts of groundwater loss obtained through quantitative assessment of groundwater infiltration showed that a higher impervious area results in higher losses. We, therefore, predict a much higher loss if similar changes in land use are realized on a nationwide scale. A plan to promote groundwater recharge in impervious areas is actively being discussed for urban areas; however, this plan is not yet applicable to farming areas. We consider it is essential to develop groundwater infiltration facilities for horticultural complexes, infiltration trenches, permeable pavements, surface water storage facilities, water purification facilities, etc. Further research and development of groundwater infiltration facilities is important for consistent utilization of water and the improvement of ecosystem services.