The management and conservation of wetlands and vulnerable protected areas of high ecological value dependent on the existence of water is complex and generally depends on the climate and rainfall in semi-arid territories such as southeastern Spain. However, one variable that is not usually considered sufficiently rigorously in this field of research is the environmental impact of the transformation of the surrounding territory due to anthropic diffuse issues. This phenomenon is not easy to appreciate, since it does not necessarily occur in the environment directly closest to protected areas and it is always difficult to measure and analyze. This study proposes an innovative spatiotemporal methodological framework to evaluate all these phenomena of diffuse anthropization whose indirect impacts on protected areas dependent on the existence of water are currently full of unknowns. Using GIS indicators, a geostatistical analysis based on the concept of the area of influence of diffuse anthropization (AIDA) is proposed to assess the spatial correlation between the anthropic transformation of the territory and the degradation of protected areas over time. The proposal has been applied with a comparative approach to three case studies located in Spain between 2000 and 2020, obtaining clarifying results on the existing spatial correlation patterns between both questions.