This paper concerns the estimation of wave run-ups on a fixed surface-piercing square column. Experiments and numerical simulations were carried out under waves of different scattering parameters and steepnesses. The results of the run-up height ratio, force coefficient, velocity field, and scattered wave profile were shown and discussed. The reasonable agreement with the experimental results indicates the capability and reliability of the numerical model in the wave run-up prediction. The nonlinearity under short waves is mainly due to the interaction between the scattered waves and the next incident wave crest, while the wave-induced flow around the column becomes more influential under long waves. These nonlinearities are further intensified under steeper waves, and the run-up height ratio increases consequently. A correction factor of 1.2–1.3 can be applied to estimate the run-up height based on the linear potential prediction, but a higher factor of 1.3–1.4 is necessary under long and steep incident waves.

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