The influence of flash flood events on the input and distribution of polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and organochlorinated pesticides (OCPs) in surface sediments from the Mar Menor lagoon were characterized in this study. These contaminants were analyzed in surface water samples collected during two flash flood events in the main surface watercourse which flow into the Mar Menor lagoon. Surface sediments were sampled semiannually before and after flash flood events. The total input of PAHs, OCPs, and PCBs (sorbed + dissolved) during two flash flood events was estimated at 0.98, 1.32, and 0.34 kg, respectively, the main input corresponding to p, p'-DDE (1.00 kg). The distribution of organic contaminants in surface sediments was not homogeneous as a consequence of the presence of many simultaneous sources and different meteorological, hydrodynamic, and physicochemical conditions. As a consequence of flash flood events, p, p'-DDE concentrations in surface sediments increased significantly in the central and south zones of the lagoon. However, in the case of PCBs, a dilution effect was observed in the south zone after such events, reducing the environmental risk. These changes in the pollutant distribution persisted at least 1 year later (autumn 2010), showing that the impact of flood events in the distribution of persistent organic contaminants in Mediterranean coastal lagoons is of relevance according to the ecological risk assessment carried out. The impact of these events should be also considered in other coastal systems, especially in semiarid and semiconfined areas.