Coastal lagoons have usually been described as the confluence of inland and marine water and classified according to their connection to the sea. These ecosystems are key elements of blue landscape connectivity and deliver multiple ecosystem services to people, including carbon storage, water provision, flood control, pollution attenuation and recreation. As their salinity regimes fluctuate significantly according to the number of freshwater inputs from surface and/or groundwater sources, underlying sediment permeability and the climate, these ecosystems may be particularly vulnerable to climate change. Previous studies in a restored Mediterranean coastal ecosystem (La Pletera salt marsh area, NE Spain) used the General Lake Model (GLM) to assess how the lagoons´ hydrological behaviors contribute not only to their salinity fluctuations but to their total water budgets. Due to limitations in acquiring empirical inflow data, a polynomial fit was used to calculate inflow and outflow data according to the observed lagoon water levels. Following this, we conducted a study using Electrical Resistivity Tomography (ERT) surveys, combined with continuous recording of electrical conductivity, temperature, and water levels of the main lagoons to determine the hydrogeological behavior of the aquifer-lagoon system and their seasonal salinity evolution. The combination of this data with the GLM has allowed us to describe and quantify the aquifer-lagoon processes, as well as to validate the application of the model in one of the main lagoons, thereby extending the knowledge on the limitations of the GLM to the global community.