Scenario and policy assessments in socioeconomic and environmental studies face significant challenges in socio-ecological systems (SES). There are a limited number of studies that have looked at the impact of different scenarios within integrated approaches, and many have used a static approach with a single driver of change. The present work analyzes the SES dynamics for a strategic basin in the Colombian Andes when implementing and analyzing scenarios and policies related to land cover and land use change using a system dynamics simulation model. The model includes natural, ecosystem services, sociocultural, and economic components. Scenarios and policy options are analyzed both individually and jointly to identify synergies or trade-off effects between the different SES components. The results showed the different trajectories of the socio-ecological system according to the cases studied, and its impact on different variables in the analyzed components. Some counterintuitive effects were also identified, such as the importance of intrinsic motivations in decision-making processes, and determinants in land management and policy design.