During the past few years the border waters between Europe and Africa have become an EU-policy crucible. In the midst of the tightening of EU border controls and refugee protection claims, supranational, national and local actors find themselves in a phase of legal insecurity and negotiation. This article is based on ethnographical research carried out in Libya, Italy and Malta. It sheds light on the different actors’ practices at sea and in the surrounding border region. It also explores how new parameters for refugee protection are emerging in the border regions of the European Union. The article argues that the policy practices of the co-operation between Italy and Libya as well as the informal operational methods carried out in the Mediterranean Sea function as a trailblazer of the overall EU refugee policy. In the long term, some of these practices will affect and change the legal basis and the formal regulations of the European refugee regime. The principle of non-refoulement could first be undermined and then abolished in this process. Using an approach that combines the empirical study of border regions with a legal anthropological perspective, the article analyses the Union’s processes of change and decision-making on local, national and supranational levels and their interconnections.