For the past few decades, jurisdictions have been using ecosystem and human health indicators to report on progress in achieving environmental policy goals. However, scholarship and practice indicate there is increasing need for governance indicators to identify gaps in policy, management and adaptive capacity. There has been significant growth in the use of governance indicators in hopes of improving outcomes in multi-level, multi-jurisdictional, multi-actor governance systems. This paper applies the OECD’s water governance indicators in two complex transboundary water governance systems in North America: the Great Lakes and Rio Grande-Bravo basins. The paper provides insights into how governance can be assessed and evaluated using water governance indicators, and highlights some of the challenges of applying governance indicators to transboundary water systems. Further, the paper reflects on how governance indicators connected to comparative and contextual analysis may serve as a foundation for a better integration of scholarship and practice.