This paper discusses definitions that have been developed and used in the study of polycentric governance. It offers conceptual refinements with the aim of reducing fuzziness, showing challenges of operationalization and application to an empirical setting—in other words, analyzing governance arrangements through the polycentricity lens. One defining element of polycentricity is the presence of “multiple decision-making centers.” This paper shows that this multiplicity is specific to the good/problem in focus, the center's tasks/responsibilities, the level in focus and analytical system boundaries. Functional overlapping among those centers is required to consider centers forming one system in relation to a good. These specificities should be examined for comparisons on polycentricity influencing the functioning of systems. The paper applies those conceptual refinements to the implementation of the EU Water Framework Directive in Berlin and Hamburg. It characterizes the two cases in terms of their polycentricity. It compares their functioning so far and how the latter relates to interactions and social interrelations. The polycentricity lens illuminates important features and differences: given an overall multiplicity of centers and a similar rule setting in both cities, the differences in the distribution of responsibilities and social interrelations led to a faster but less integrated implementation in Hamburg than in Berlin. The application of the proposed refinements yields insights into further work to be done in favor of theory-building on the functioning of polycentric governance systems.