The combination formed by the intense transformation of the territory and climate change in the Spanish Mediterranean basins has configured an explosive cocktail from the point of view of the risk of flooding in these areas. Climate change is making intense DANA (Spanish acronym of depresión aislada en niveles altos) type rains a more frequent phenomenon in Mediterranean basins. The vulnerability of the coastal territory in these areas as a consequence of the DANA phenomenon now requires the authorities to implement new strategies and policies that reduce the significant economic damage and loss of human life suffered in recent years. However, correlating these two phenomena with the increased risk of flooding is a difficult problem to diagnose, and even more difficult to solve. For this reason, a structured GIS methodology is proposed based on a geostatistical indicators analysis that correlates the transformation of the territory with the increase in vulnerability due to floods. The assessment of the validity of a proposed methodology is applied to the case study of the Campo de Cartagena watershed located around the Mar Menor, a Mediterranean coastal lagoon in Southeastern Spain. This area has suffered three catastrophic floods derived from the DANA phenomenon between 2016 and 2019.The results show that apart from the effects derived from climate change, the real issue that amplifies the damage caused by floods is the diffuse anthropization process in the area, which has caused the loss of the natural hydrographic network that traditionally existed in the basin. Based on the results obtained in this analysis, risk mitigation actions will be proposed through the improvement of land management by using of nature-based solutions.