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A thorough understanding of long-term temporal social-ecological dynamics at the national scale helps to explain the current condition of a country's ecosystems and to support environmental policies to tackle future sustainability challenges. We aimed to develop a methodological approach to understand past long-term (1960-2010) social-ecological dynamics in Spain. First, we developed a methodical framework that allowed us to explore complex social-ecological dynamics among biodiversity, ecosystem services, human well-being, drivers of change, and institutional responses. Second, we compiled 21 long-term, national-scale indicators and analyzed their temporal relationships through a redundancy analysis. Third, we used a Bayesian change point analysis to detect evidence of past social-ecological thresholds and historical time periods. Our results revealed that Spain has passed through four social-ecological thresholds that define five different time periods of nature and society relationships. Finally, we discussed how the proposed methodological approach helps to reinterpret national-level ecosystem indicators through a new conceptual lens to develop a more systems-based way of understanding long-term social-ecological patterns and dynamics.