The Mar Menor is the largest lagoon along the Spanish Mediterranean coast. It suffers from eutrophication and algal blooms associated with intensive agricultural activities and urban pressure in the surrounding Campo de Cartagena plain. A balanced discharge of groundwater, carrier of algal nutrients such as nitrate, is essential to ensure the integrity of the coastal lagoon and the availability of groundwater resources inland. In this work, we present a 3D hydrogeological model of the unconfined Quaternary aquifer that discharges into the lagoon. The model couples both surface water balance and groundwater dynamics and has been calibrated to available data in the period 2000–2016. The calibrated model allows understanding of the current state of the aquifer and its link to the lagoon. The potential discharge has been quantified in both space and time and falls between 69.5 and 84.9 hm3/yr during dry and wet periods, respectively (with values of nitrate discharge of 11.4–11.8 Mkg/yr in the absence of aquifer sink terms, e.g., leakage to deeper aquifers and pumping from groundwater wells). The predictive capabilities of the calibrated model can be used to test the impact of different integrated management scenarios on the surface-groundwater dynamics of the catchment. Three plausible management scenarios are proposed that include localized and distributed groundwater pumping (drains and groundwater wells, respectively). Results show the effectiveness of the scenarios in reducing the groundwater and nitrate discharge into the lagoon. The disadvantages of the proposed scenarios, including potential seawater intrusion, need to be balanced with their relative merits for the sustainable development of the region and the survival of the Mar Menor ecosystem. The modelling approach proposed provides a valuable tool for the integrated and holistic management of the Campo de Cartagena-Mar Menor catchment and should be of great interest to similar hydrological systems with high ecological value.