Integrated Coastal Management (ICM) aims to ensure sustainable management of coastal areas. The Systems Approach Framework (SAF) provides a structure for an ICM process that includes scenario simulations of management options for complex systems. Through the SAF stakeholders are identified and engaged at an early stage. Further, the SAF guides a process to assess the ecological sustainability, economic efficiency, and social equity of management options, even for complex issues. Implementation of the European Union's Birds Directive (BD) in 1979 instigated protective management plans to protect a waning population of cormorant (Phalacrocorax carbo sinensis). Since then, multiple adjustments were made to the management plans to mitigate arising issues and conflicts. In this study, we used the SAF to conduct a retrospective analysis of cormorant management in Europe, Denmark, and a local community in order to identify which ICM elements were put into effect and their effectiveness. The analysis comprised the two initial steps of the SAF: Issue Identification and System Design. Data and information were extracted from EU and Danish management plans, available literature and interviews with stakeholders. The management process was divided into two periods related to the motivation: i), 1979–2002 focusing on cormorant protection promoted by nature conservations organisations, and ii), 2003–2020 focusing on ad hoc adaptive management to mitigate negative effects of an exponentially increasing cormorant population on other sectors and related income and activities. Our study revealed that cormorant management at all levels lacked elements important for a sustainable ICM process. Implementation of the BD was a top-down process leading to a single sector solution, influenced by a few highly organised stakeholders with strong views. The ecological issue of protecting the species was resolved, but the lack of Systems Thinking and specific success targets, for which indicators could have been developed, led to new conflicts and negative user perceptions. In response to increasing and new emerging conflicts, more stakeholders became involved during the second period. Thorough mapping of stakeholders, institutions and governance structures at the outset could have provided for a more transparent, inclusive, and participatory process. In addition, the management plans did not involve cross-sectorial, bio-economic assessments. The latter would have allowed deliberations of potential ecological and socio-economic consequences of different management options, which could have enhanced transparency and equity in the decision-making and thus could have facilitated compliance and long-term sustainability during implementation.