The bank protection measures of waterways shall become more environmentally friendly in the future including the use of plants instead of stones. The low levels of protection provided by plants in the early phase after planting requires a process-based understanding of soil-wave-interaction. One process that is considered essential is liquefaction where the soil undergoes a phase-change from solid-like to fluid-like behaviour which could reduce the safety of the system. The aim of this publication is to analyse the results of column experiments on wave-induced soil liquefaction and to develop a numerical model which is able to describe the entire process from the pre-liquefaction phase to the following reconsolidation in order to support the analysis of liquefaction experiments. Numerical simulations of the column experiments were done using a fully coupled hydro-mechanical model implemented in the open-source software FEniCS. A permeability model derived from granular rheology allows the simulation of dilute as well as dense suspensions and sedimented soil skeletons. The results of the simulations show a good agreement with the experimental data. Theoretical limits in the liquefied state are captured without the common modelling segmentation into pre-and post-liquefaction phase. Due to the modular structure of the implementation, the constitutive setting can be adjusted to incorporate more complex formulations in order to study the influence of wall friction and non-linearity in soil behaviour.