Low-lying coastal estuaries are particularly vulnerable to environmental threats including saline water intrusion and surge inundations. These risks are worsened by factors such as sea-level rise, excessive groundwater extraction, and extreme weather events, which threaten freshwater availability and coastal infrastructure. To mitigate inundation impacts, various facilities such as river embankments, pumping stations and drainage systems are implemented to manage water levels, to increase agricultural productivity, and to protect areas from flooding. Even though these facilities provide essential flood control, they may have unintended consequences on groundwater dynamics, potentially altering surface-subsurface water interactions and exacerbating salinization risks. To better understand these impacts, we aim to investigate how the flood mitigation facilities affect groundwater salinity in the low-lying estuary of Kujukuri plain, Japan, using a numerical approach, i.e., HydroGeoSphere. Due to ongoing land subsidence in this area, the pumping stations and ditch systems were built to prevent flooding and manage the resulting land surface elevation changes. Here, we developed scenarios to assess the effects of these mitigation facilities on groundwater salinization, considering (a) the case before land subsidence, and (b) the case where land subsidence occurs, using current elevation data and the addition of pumping stations. The simulation results show that when pumping stations work effectively, groundwater levels can be lower than the tidal river level, leading to seawater intrusion from the tidal river through subsurface. As a result, groundwater salinization extended further into the lowland areas on both sides of the tidal river. This finding indicates that mitigation facilities can effectively prevent inundation, yet they may worsen groundwater salinization. The study implies the importance of evaluating flood prevention strategies as their unexpected results could compromise groundwater resources.