Governance networks are both nested and interconnected systems. Identifying internal boundaries within governance networks, such as those governance structures that influence and are influenced by large and diverse watersheds such as the Lake Champlain Basin, is necessary for differentiating between multiple functional subnetworks. Internal network boundaries exist between functional subnetworks when the networks have divergent structures (Weible & Sabatier, 2005). A qualitative case study of Lake Champlain Basin watershed governance networks identified several key overlapping subnetworks in which organizations interact in a variety of ways (Koliba, Reynolds, Zia, & Scheinert, 2015). An online survey of institutional actors was used to identify which actors were connected in five different functional subnetworks. Structural comparisons are made by analyzing the correlation between the subnetworks based on the quadratic assignment procedure (QAP) and network macrostructure. Results show that the information sharing, technical assistance, and project collaboration subnetworks formed one grouping, while the reporting and financial resource sharing subnetworks formed another g rouping. The results demonstrated that this triangulated comparison was necessary to reach valid conclusions on the structural variation between the subnetworks on a multiplex network when subnetworks were structurally similar.