Storm Xynthia crossed France’s western coast between 28th February and 1st March 2010. It hit the Vendée and Charente-Maritime departments hardest, as storm surge flooded up to 23,000 ha of coastal agricultural areas (i.e. polders), causing severe damage to farming operations. However, farm-level damage in the aftermath of seawater flooding is an issue that has rarely been explored in the literature. Here we investigated the effects of storm Xynthia on agriculture at the farm scale. We focused on the case study of Saint Laurent de la Prée research farm, a mixed crop–livestock system that was severely hit. All damages were described and economic losses were quantified for the years 2010 and 2011. The results show numerous consequences of the storm in terms of crop and fodder production losses, but also farm infrastructure repairs, crop restoration and animal health problems. Economic damage costs were high, reaching €71,720 in 2010 (€500/ha flooded) and €56,195 (€390/ha) in 2011 for the case study farm. The discussion highlights the farm-level impacts of seawater flooding and the crucial factors that can explain the damage caused to agriculture by storm events in coastal areas. The results are also discussed in the wider context of global warming which is expected to cause sea level rise and more frequent storm events in the future. The vulnerability of coastal agricultural areas to storms thus exposes broader issues of coastal flooding risk management and specifically the allied protection–remediation–adaptation measures. The conclusions underline the need for future research to address prospective scenarios and subsequent adaptive strategies.