Human pressures on ecosystems have increased significantly over the last decades, and especially Mediterranean coasts are strongly impacted by the development of big cities and industrialized area, such as the Bay of Marseille. Prior to any investigations on ecological or contamination impacts, it was necessary to understand sediment dynamics and its response to natural extreme events such as storm or heavy rainfall events. In situ observations were dedicated to understand the behavior of bed sediments, and their spatial distribution. A benthic station was deployed for three months to observe the impact of extreme events on hydrodynamics and sediment dynamics in a critical zone of the study area. These measurementswere used to calibrate and validate the RHOMA MARS3D/WWIII configuration, both in terms of hydrodynamics, waves and sediment dynamics. Numerical simulations were then analyzed in order to examine the influence of extreme meteorological events on the Marseille coastal physical ecosystem.