The Southern Taiwan Science Park (STSP) is located between Hsinshi Township and Shanhua Township of Tainan County, with the newly-built, high-speed railway running through its eastern side. The low-frequency vibration which was generated by passing high-speed trains causes environmental disturbances to industries within the Park. To address this issue, the implementation of vibration-reduction project with detailed design and construction was provided. The diaphragm wall-type vibration reduction walls will be built along the borderline between Hsinshi Township and Shanhua Township to reduce the impact on industries. The diaphragm wall structure will block groundwater from flowing to affect the underground hydrology. This study was aimed to discuss and assess the best configuration for the vibration reduction effects and environmental impacts. Numerical analysis of the impacts on groundwater hydrology was conducted in two cases. The simulation results indicated that both sides of diaphragm walls developed gaps in groundwater levels. Hence, diaphragm walls effectively reduced adverse impacts on groundwater hydrology with openings at locations where underground pipelines ran. Such variations were within the scope of groundwater level of high water and low water periods. Therefore, surface runoff and land subsidence resulting from the diaphragm wall construction were not severe. As diaphragm walls were made of impermeable materials, pumping water nearby made the groundwater level drawdown effects worse. Groundwater level variations resulting from pumping water were far greater than the regional groundwater level variations after the establishment of diaphragm walls. Special attention must be paid to this situation in follow-up management.