This paper discusses the governance of port classification through the lens of multi-level governance theory, with a particular focus on the Port of Aalborg and the issue of classification of Limfjord waters, in Denmark. The study identifies a conflict in which national governmental decisions regarding the classification of navigable waterways obstruct the port's access to funding opportunities. Despite the port's autonomous operational capacity, national control over waterway classification and port typology shows a nested governance dynamic, thereby highlighting the intricacies of the European Union's subsidiarity principle. This paper argues that the case illustrates how the classification of inland waterways, although ostensibly legal, is intrinsically political and subject to national interests. The Danish government's refusal to designate the Limfjord as a navigable waterway potentially hinders regional development and impedes the EU's policy objectives for intermodality. Methodologically, the research synthesizes desk-based analysis with key-informant interviews to examine the legal, political, and geographical dimensions of this issue. The findings contribute to multi-level governance theory by describing the case as a hybrid model that integrates both nested and polycentric elements, thereby enriching the debate on governance complexities within the European context.