AbstractGroundwater hydrodynamics are significantly affected by the capillary effect when groundwater table approaches sand surface. A complex effective porosity was suggested to replace the specific yield to represent the capillary effect based on varieties of sand column experiments, and its estimation is based on the assumption that the response of time‐varying groundwater table is a simple harmonic motion. Nevertheless, groundwater hydrodynamics always consist of multiple harmonic components, which should be further examined. In this study, we first conducted laboratory sand column experiments with respect to different periodic oscillation conditions. Then, a fast Fourier transformation algorithm was applied to analyze the measured groundwater table, upon which the high order harmonic components under high frequency wave conditions was demonstrated. Subsequently, based on a perturbation approach, we presented a third order analytical solution of time‐varying groundwater table under a simple harmonic oscillation. The gradient descent method was applied to estimate the complex effective porosity by fitting the high order analytical solution to the experimental data. In addition, effects of various parameters, representing different driving head conditions and sediment properties, were testified through parametric studies, which demonstrates high order harmonic components should not be neglected under the conditions of large relative amplitude of driving head, short period oscillation, and the ratio of hydraulic conductivity to dynamic effective porosity being around 1 m/s, for example, in the scenarios of wave‐dominant swash zone. These new findings are of great importance to extend our understandings of the capillary effect on groundwater hydrodynamics.