Against the backdrop of climate and environmental pressures, as well as limited resource availability and trade conflicts, devising policies for energy and the use of natural resources in general becomes exceedingly complex. Moreover, policies are required to account for interrelations between individual resources and between different sectors and policy fields, but implementation often lacks. To evaluate the current state of integrated policy design in the EU, a review of European energy, water, and agricultural policies was conducted. Using a qualitative comparative research approach, the objective was to identify and explain the differing degrees and variations in policy integration among them. To this aim, the concepts “Environmental Policy Integration” and “Water-Energy-Land Nexus” were jointly applied as analytical frameworks. The analysis revealed that currently, different authorities are endowed with largely sectoral mandates. Accordingly, the respective sectoral policy sets are historically grown based on differing sets of formal and informal rules and processes, thus making policy integration among the sectors, let alone within the nexus, a highly challenging task.