Coastal areas are witnessing a surge in critical infrastructure development, such as sea-crossing bridges, to support growing populations and economic activities. However, these structures face ongoing challenges in harsh marine environments. Therefore, understanding the hydrodynamics of bridge structures under extreme freak wave conditions is imperative for designing effective countermeasures. This study investigates pier hydrodynamics using a three-dimensional numerical flume simulated by OpenFOAM, focusing on loading characteristics and wave climb differences under freak and linear waves. Results show that freak waves induce larger surges and forces compared to linear waves, with a notable “bell vibration” effect near the wave surface. Moreover, peak forces and bending moments increase nonlinearly with the wave height-to-significant wave height ratio. For double-column piers, transverse alignment concentrates wave climb on the rear side of the front pier, with forces increasing with spacing, while those on the rear pier decrease. Conversely, longitudinal arrangements show amplified loading effects. These findings provide valuable insights into the hydrodynamic behaviour of bridge piers under freak wave conditions, offering practical implications for the design and protection of sea-crossing bridges.