Stakeholder analysis as a specific tool in social science can be used to explain why environmental conflicts arise or persist and identify steps to resolve these. This paper considers the conflict over the great cormorant, a fish-foraging bird with a rapidly growing population, a conflict previously treated only at a local, subnational or national level. The measures taken have sometimes mitigated the conflict, but have not addressed the damage and conflicts owing to the rapid cormorant population expansion. As the population is mobile at the scale of Europe, management of the population needs to be considered at the European level. In the 1990s, the Convention on Migratory Species (CMS) drew up a management plan, which was never endorsed. Interviews with authorities, scientists and other stakeholders revealed they considered the CMS management plan inappropriate because some thought it compromised national autonomy while others thought there was insufficient cormorant protection. A possible step-wise solution to developing a pan-European management plan is proposed, requiring agreement on common objectives and strategies.