The comparison of a morphodynamic model results with observations is an essential part to establish its credibility. In the past multiple model were validated against observations for sand banks, coastlines or estuarine environments. Some modelling have studied the marine dunes migrations but are generally limited to a two-dimensional study. In the present study, a three-dimensional morphodynamic model were setup on an area where highly dynamic dunes are present. The modelling results were analysed and compared to in-situ observations either using a 2D and a 3D method. The vertical and horizontal differences with observations were then assessed using the known method and, based on these results, an updated validation method were proposed to overcome some issues that could interfere with the process.