This study presents field and modelling data of how dense seawater plumes move into a shallow coastal freshwater aquifer, following a storm flooding event. The locations of these seawater plumes appear to be controlled by topographical depressions where seawater ponds were observed after the flooding. The rapid development and sinking of these seawater plumes in the aquifer were monitored by pore water electrical conductivity measurements in a 120-m transect of about 100 piezometers, and by drive-point continuous vertical resistivity logs (el-logs). Large parts of the plumes reached the bottom of the aquifer 10 mbs in less than 30 days, but the plume migration caused by the unstable density distribution was found to be highly variable. The variable density code SUTRA was used for numerical modelling of the flow of seawater down into the aquifer. The model captures the overall trends of the plume development and migration velocity observed in the field. However, even after introducing measured medium-scale heterogeneity in the model, it could not adequately describe the complex details in the seawater distribution. This variability is believed to be caused by the geological heterogeneity and much of the variability appears to be on a small scale (∼ cm), finer than the sampling scale of this study. The vastly different chemical composition of the seawater compared to the fresh groundwater triggered several geochemical reactions in the affected part of the aquifer. The high seawater sulfate content shifted the dominating redox-process from methanogenesis to sulfate reduction. The results of this field and modelling study highlight the complexity of how an aquifer, subject to seawater flooding, is contaminated by seawater. In turn, the results give insight into the vulnerability of coastal freshwater aquifers to catastrophic flooding events and to future sea-level rise. The study also indicates how other groundwater contaminants in dense fluids released at the surface may spread in the aquifer, and, points to the possible use of density-driven flow as a novel method to introduce reactants for remediation at contaminated sites.