Resource management boundaries seldom align with environmental systems, which can lead to social and ecological problems. Mapping and analyzing how resource management organizations in different areas collaborate can provide vital information to help overcome such misalignment. Few quantitative approaches exist, however, to analyze social collaborations alongside environmental patterns, especially among local and regional organizations (i.e., in multilevel governance settings). This paper develops and applies such an approach using social–ecological network analysis (SENA), which considers relationships among and between social and ecological units. The framework and methods are shown using an estuary restoration case from Puget Sound, United States. Collaboration patterns and quality are analyzed among local and regional organizations working in hydrologically connected areas. These patterns are correlated with restoration practitioners' assessments of the productivity of their collaborations to inform network theories for natural resource governance. The SENA is also combined with existing ecological data to jointly consider social and ecological restoration concerns. Results show potentially problematic areas in nearshore environments, where collaboration networks measured by density (percentage of possible network connections) and productivity are weakest. Many areas also have high centralization (a few nodes hold the network together), making network cohesion dependent on key organizations. Although centralization and productivity are inversely related, no clear relationship between density and productivity is observed. This research can help practitioners to identify where governance capacity needs strengthening and jointly consider social and ecological concerns. It advances SENA by developing a multilevel approach to assess social–ecological (or social–environmental) misalignments, also known as scale mismatches.