The provisions in the Habitats Directive relating to protection of sites establish a triumvirate of decision-makers: administrative authority, scientific advisor, and judiciary. This paper examines the relationship between these decision-makers as developed in recent case law, both at a European and national level. It argues that reference to the goal of environmental protection obscures the allocation of power amongst these actors, and that to truly understand the resulting system, we must acknowledge the differing norms which motivate each of these actors. In particular, it argues that we must consider the judiciary as an actor within the decision-making process, and should examine the role of the principles of judicial review and European law in shaping this. It highlights that there are currently conflicts within the process, and that the principles of judicial review cannot provide a successful mechanism to manage these conflicts without an explicit consideration of the values “hidden” therein.