The North Sea is one of the most economically important seas in the world due to productive fisheries, extensive oil and gas fields, busy shipping routes, marine renewable energy development and recreational activity. Unsurprisingly, therefore, the use of marine protected areas (here defined widely to include fisheries closed areas and no-take marine reserves) in its management has generated considerable controversy-particularly with regards to the design of a regional ecologically coherent MPA network to meet international obligations. Drawing on three MPA processes currently occurring in the UK North Sea, we examine the real-world problems that make the designation of MPA networks challenging. The political problems include: disagreement among (and within) sectors over policy objectives and priorities, common access to fisheries resources at the EU level increasing the scale at which decisions have to be made and lack of an integrated strategy for implementing protected areas in the North Sea. The scientific problems include the patchy knowledge of benthic assemblages, limited knowledge of fishing gear-habitat interactions, and the increased risk of unforeseen externalities if human activity (predominantly fishing) is displaced from newly protected sites. Diverging stakeholder attitudes to these problems means that there is no consensus on what ecological coherence actually means. Ultimately, we caution against 'quick-fix' solutions that are based on advocacy and targets, as they create confusion and undermine trust in the planning process. We argue for a more pragmatic approach to marine protection that embraces the complexity of the social and political arena in which decisions are made.