Abstract: Reinforced concrete (RC) rectangular hollow piers are characterized by their low self-weights and superior aseismic performances, which make them widely adopted in bridge constructions. Efficiently estimating their seismic hydrodynamic effects provides a reliable basis for aseismic design. This study establishes a numerical method for fluid-structure interactions under earthquakes and validates it using underwater shaking table tests. It conducts numerical simulations to investigate the seismic responses of RC rectangular hollow bridge piers in water, examines how the pier height-to-width ratio, water depth, cross-sectional aspect ratio, hollow ratio, and the mass at the top of the pier influence seismic hydrodynamic effects, and develops an extreme value estimation model for predicting the maximum seismic hydrodynamic effects. The research results indicate that increases in the water depth, in the cross-sectional aspect ratio, and in the hollow ratio amplify the peak responses of relative displacements, of bending moments, and of shearing forces in bridge piers. Notably, the water depth and section hollow ratio have a more significant impact on the hydrodynamic increase, with effects exceeding 90% and 110%, respectively. Increasing the mass at the top of the pier reduces seismic hydrodynamic effects. When the height-to-width ratio is large, the hydrodynamic amplification effect exceeds 10% and cannot be ignored. The proposed model for estimating extreme hydrodynamic effects induced by earthquakes is highly efficient, achieving a maximum estimation error of 12.5%. It can therefore provide a useful reference for the aseismic design of deep-water bridge piers.