Differences in the degree of saturation in soil layers, from the time the soil properties were measured to the time an earthquake occurs, can influence seismic site response observations. To investigate the potential influence of variations in groundwater levels, equivalent linear analyses were performed whereby the groundwater table was changed and soil properties were subsequently adjusted for each scenario. Data from the Kiban-Kyoshin (KiK-net) network of surface-downhole seismometers were used as the baseline for the validation of numerical analyses. Surface-to-rock ratios of response spectra and Fourier transfer functions were numerically calculated for different groundwater level scenarios. Unsaturated soil conditions were modeled by increasing the suction and effective stress in the vadose zone. Stronger ground motion amplifications were observed when the groundwater water level was lowered. This trend is associated with simultaneous effects of shear modulus, damping, and unit weight on seismic response of soil profiles with different groundwater levels.