Sea state can influence the turbulent air–sea exchanges, especially the momentum flux, by modifying the sea‐surface roughness. The high‐resolution non‐hydrostatic convection‐permitting model MESO‐NH is used here to investigate the impact of a more realistic representation of the waves on heavy precipitation during the Intense Observation Period (IOP) 16a of the first HyMeX Special Observation Period (SOP1). Several quasi‐stationary mesoscale convective systems developed over the western Mediterranean region, two of them over the sea, and resulted in heavy precipitation on the French and Italian coasts on 26 October 2012. Three different bulk parametrizations are tested in this study: a reference case (NOWAV) without any wave effect, a parametrization taking into account theoretical wave effects (WAV) and a last one with realistic wave characteristics from the MFWAM analyses (WAM). Using a realistic wave representation in WAM significantly increases the roughness length and the friction velocity with respect to NOWAV and WAV. The three MESO‐NH sensitivity experiments of the IOP16a show that this surface‐roughness increase in WAM generates higher momentum fluxes and directly impacts the low‐level dynamics of the atmosphere, with a slowdown of the 10 m wind, when and where the wind speed exceeds 10 m s−1 and the sea state differs from the idealized one. The turbulent heat fluxes are not significantly influenced by the waves, these fluxes being controlled by the moisture content rather than by the wind speed in the simulations. Although the convective activity is globally well reproduced by all the simulations, the difference in the low‐level dynamics of the atmosphere influences the localization of the simulated heavy precipitation. Objective evaluation of the daily rainfall amount and of the 10 m wind speed against the observations confirms the positive impact of the realistic wave representation on this simulation of heavy precipitation.