The objective of the OPAL (ref: PID2019-110311RB-C22) project is to identify and assess the major pathways delivering nutrients, trace metals and pollutants originated from anthropogenic activities to coastal Mediterranean lagoons connected to intensively used aquifers and their consequences on the lagoon geochemical cycles. One of its goals is “To assess of the role of storms and episodic events in the input of nutrients, metals and pollutants”. Within this framework, the capability of the hydrodynamic model Regional Ocean Model System (ROMS) to simulate fast increase of the Mar Menor coastal lagoon sea level due to extreme flood was tested. In September 2019 the stronger storm and flood registered in the Spanish Levantine area in 87 years occurred. In only 13 hours the sea level of the Mar Menor hypersaline lagoon of 135 Km2 increased 0.6 meters, thus creating a strong halocline due to the fresh water that entered from the floods. The sea level took near 7 days to restore. The morphology of the three outlets communicating the lagoon with the Mediterranean Sea determined their water flux going out the lagoon. This kind of extreme events produces significant enhancements of the inputs of nutrients, metals and pollutants to the lagoon water column coming from an intensive agriculture watershed. To understand the hydrodynamics behind this phenomenon, the ROMS model was used to simulate this episode. Simulations were validated against sea level, salinity and temperature recorded in the water and included surface water inflow from the land, wet/dry areas, bidirectional nesting, water exchange with the Mediterranean Sea and air/water interaction. The result obtained show the robustness of ROMS simulating this kind of events with two layer halocline system formed due to the fresh water inflow from land in a hypersaline water mass.