This study explores how to use techniques of prospective analysis in order to incorporate dynamic factors that put into risk the persistence of biodiversity into systematic conservation planning. Land use and cover change (LUCC) and climate change (CC) represent the main impacts and future threats to biodiversity and thus were the subject of analyses that provided information on prioritization for conservation actions. Since LUCC, CC and biodiversity loss, as well as the related socio-economic structures take place on a regional scale, this work is based on a large watershed in southern Mexico, the Grijalva-Usumacinta Basin. This basin is not only one of the most important areas for biological diversity, but is also renowned for its cultural complexity and hydrological importance and the multiple environmental and social problems that put biodiversity in peril. The main finding is that deforestation and forest degradation are the main LUCC processes and their high rates and strong future trends make it difficult to get to the point of forest transition in the near future, when deforestation and regeneration are balanced. Nevertheless, the scenario analysis shows that it is possible to influence LUCC trajectories in a substantial way in order to halt negative effects over biodiversity in the next decade. CC represents an additional threat to biodiversity difficult to evaluate, especially if the multiple synergistic effects between CC and LUCC are considered that could lead to much higher impacts. Anyway, the analysis showed that even until 2030 CC could have impacts on bioclimatic variables and species composition that could further hamper conservation efforts in the study area. Criteria for a proactive prioritization of sites for conservation are proposed based on scenarios of LUCC and CC. These criteria are used to identify “hot spots” (high probability of LUCC and severe CC impacts) and “refuges” (high probability of permanence and minor CC impacts). This joint analysis of CCUS and CC shows that there are differences between the conservation and the probable scenario; the effort needed to conserve the biodiversity contained in the priority sites in the conservation scenario is considerable less. The spatial pattern of hot spots and refuges of change is very similar across scenarios, despite the differences in absolute areas compromised by each.
