Groundwater degradation is a global problem linked to irrigation agriculture and aggravated by climate change. In drylands, where aquifer recharge is low, irrigation has emerged as an engine of economic growth. This problem falls under the paradigm of desertification, as it fits the definition of this complex problem in that the degradation of drylands is due to climatic variations and inappropriate human activities. Land Degradation Neutrality (LDN), the response of the United Nations Convention to Combat Desertification to the lack of progress in tackling desertification, is integrated into Sustainable Development Goal 15.3 and provides the adequate framework for implementing effective solutions. LDN prioritizes prevention strategies, and early warning systems coupled to integrated simulation models is a sound approach. We analyze the dynamics of a coastal aquifer in southern Spain, a “desertification landscape” according to the Spanish National Action Plan to Combat Desertification. For this purpose, we have (i) adapted a generic desertification model that considers socio-ecological systems as a particular case of predator-prey systems; and (ii) coupled to this model a risk analysis to calculate the probabilities of groundwater salinization under the current scenario of water resources use, driven by the expansion of greenhouse agriculture supported by external water transfer. The risk of desertification is close to 100%: groundwater salinity is 40 dS m-1 (well above tomato tolerance, 3.5 dS m-1), and 2.4 Mm3 yr–1 water transfer is needed to support the 631 ha of greenhouses. This worrying result suggests that complimentary solutions should be promoted to deactivate the ongoing process of desertification. Among them, we propose reclaimed water, diversifying the economy, or promoting crops adapted to aridity. This simulation framework shows how to explore the future of a socio-ecosystem under current scenarios and others that consider climate change, the energy crisis, or the impact of alternative solutions.