Abstract: Based on the dynamic centrifugation technique, two groups of model tests are designed and performed, and the geotechnical free field simulation arrays with and without water are restored and reproduced. The white noise sweep and El Centro waves with different intensities are used as the base input of the shaking table, and the traditional spectral ratio method considering cancellation interference is used to obtain the site response results of two groups of free field models under different working conditions. Through the comparative analysis of the modal response characteristics and basic period differences between watery and anhydrous sites, the function and influences of overlying water in estimating the basic period of the site are evaluated and summarized. The results show that due to the influences of the dead weight stress of overlying water, the surface peak magnification of the anhydrous model is higher than that of the watery model, and the surface time history waveform of the anhydrous model is sparse, indicating that the surface seismic waves have abundant high frequency components. Whether it is the white noise sweep or the base loading mode of El Centro wave, there are significant differences in the basic period and mode amplification factor of the two groups of free field models with and without water, indicating that the overlying water has a certain influence on the estimation of the basic period of the seafloor complex medium system, and the maximum deviation of the basic period of the land model and the sea model is 35.5%.