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Coastal freshwater resources are commonly under high risk of being contaminated from seawater. The main processes that affect seawater intrusion are groundwater overexploitation, land use change, and climate change effects. In this context coastal lagoons represent the more sensitive environments prone to seawater intrusion. Numerical modelling is a useful tool to understand and predict seawater intrusion. In this study, a three-dimensional SEAWAT model is employed to simulate the seawater intrusion to coastal aquifers of Variconi Oasis (Italy). The present simulation was divided into a calibration and a validation model, then the model was used to predict the salinization trend up to 2050. Results show the role of the sea in salinizing the beach front, while the retrodunal environment is characterized by transitional environments. Future seawater intrusion scenarios considering only climate data showed no significative differences in respect to the actual situation. The same happens considering also a low sea level rise prediction. On the contrary, the worst scenario (high sea level rise prediction), depicts a quite different situation, with a saline intrusion in the Variconi oasis that will severely affect the fragile transitional ecosystem. This modelling framework can be used to quantify the effects of climate changes in similar coastal environments.