Participatory Integrated Assessment (PIA) has become a vital tool for decision-making for sustainable development, but it faces significant challenges due to the inherent uncertainty of socio-ecological systems. Uncertainty arises from multiple sources, such as incomplete data, knowledge gaps, and unpredictable events, which can lead to inadequate risk estimations and potentially undermine the effectiveness of environmental planning efforts. To address these challenges, this study proposes a qualitative modeling approach for risk estimation in PIA. The approach employs Decision Making under Deep Uncertainty (DMDU) to combine qualitative insights and information from stakeholders with available quantitative data. It allows for the exploration of alternative future states of the world and the identification of robust scenarios that promote sustainable development. The effectiveness of the proposed approach is demonstrated through the Ecological Ordinance of Yucatán, Mexico, a policy-making tool for multi-sectoral environmental planning. The study shows how qualitative DMDU can identify critical uncertainties and provide insights into regional management strategies. It also emphasizes the importance of stakeholder engagement and transparency in the decision-making process. Overall, this study presents a promising approach for addressing multiple forms of uncertainty in PIA and improving ecological risk estimation for decision-making in complex socio-ecological systems.