To enable robust and just sustainability pathways, we need to understand how social-ecological systems (SES) respond to different governance configurations, considering their historical, institutional, political and power conditions. We advance a robust methodological tool for the integrated analysis of those conditions, focusing on SES traps and building on an existing case study: the Doñana region (Guadalquivir estuary, SW Spain), an estuary-delta SES. Doñana is characterized by institutional rigidity for water resources and wetland conservation governance and, more generally, by a SES rigidity trap. Here, we focus on a relatively recent hydraulic megaproject involving deep dredging in the Guadalquivir estuary, finally canceled due to its broad negative socioeconomic and environmental repercussions. Our methodological development consists of a novel combination of the politicized version of the Institutional Analysis and Development (pIAD) framework and the Networks of Action Situations (NAS) approach. Our analysis reveals a governance configuration characterized by strategic interactions among key actors posing no new large socioeconomic or environmental risks in the short term. This pattern is however vulnerable due to an underlying coordination failure and sub-optimal equilibrium situation, which emerge from a pattern of uncooperative behavior that cannot be explained without considering discourse inertia and power dynamics. Deep dredging could have led to a sudden fall of governance into a below sub-optimal equilibrium and regime shift toward a lock-in trap posing high sunk and trajectory-shifting costs. Currently, the game is on for achieving a shift to a high ‘blue equilibrium’ and launching a robust sustainability pathway through collective action.