The driest area of Europe is located in the south-east of Spain. In this region, water plays an essential role for the development and maintenance of the major economical engines for society, tourism and agriculture. In the coastal areas, water scarcity increases the risk of saltwater intrusion connected also to the overexploitation of aquifers. The adequate management of coastal aquifers requires to integrate climatic and hydrogeological information, but it is common to find incomplete datasets and uncertainties about the sources and sinks of water. The Torrevieja coastal aquifer gathers all these challenges with limited information available and essential questions about the aquifer functioning. The water budget has an imbalance between inputs from precipitation–irrigation return and outputs connected to water supply pumping for population and agriculture. Initial estimates indicate an annual deficit of 4.36 Mm3 that would produce short-term changes in the hydrodynamic system. However, the aquifer has been continuously exploited for the last 30 years which indicates the necessity of reviewing the hydrogeological characteristics of the region. A set of new conceptual models has been tested with numerical models to present alternative possibilities about the hydrogeological functioning combined with the analysis of hydrochemical data. The evaluation of the conceptual models revealed that up to 75% of the groundwater being extracted could proceed from a lower aquifer that has not been monitored. The improved water budget indicated a much lower annual deficit in the Torrevieja aquifer (0.2–0.8 Mm3) occasionally positive in years with high precipitation but introduces new questions about the recharge and origin of groundwater in the lower aquifer. In semi-arid areas, water is crucial facing climatic change and desertification processes; in this work, it is presented how the use of numerical models combined with hydrochemical information is a useful approach to provide new perspectives and improve water management.