Some ecosystem services (nutrient removal and biodiversity conservation) in the wetlands surrounding the Mar Menor (southeastern Spain), the largest coastal lagoon in the western Mediterranean, have been assessed. A dynamic system model was developed to estimate the dynamics of nutrients, the role of wetlands in nutrient removal, and the final inputs reaching the lagoon. The socioeconomic issues, such as land use changes and seasonal dynamics of the tourist population, are part of the variables defining the model. The model tracks the increase in irrigated lands and the associated increased nutrient inflows, causing the eutrophication of the lagoon and favoring summer jellyfish outbreaks. The model was applied to test several management options to reduce the point and diffuse pollution and showed that the use of the Mar Menor wetlands would be the measure achieving the highest nutrient removal. A cost-effective analysis (CEA) has shown that this is also the most cost-effective of tested measures. The dynamic model and the CEA analysis have allowed a first economic valuation of some of the avoided costs of this ecosystem service. However, particularly in arid environments, there may exist a trade-off between the nutrient removal functionality of wetlands and the preservation of their biodiversity, dependent on high salinity and scarce flows of water and nutrients. This demands adequate and cost-effective solutions that acknowledge such trade-off. One option is to spatially differentiate both functions by keeping present wetlands without additional flows and by restoring previously lost areas of wetland for such nutrient removal service.