The National Estuary Program (NEP) in the United States is a promising approach to managing estuaries. This program aims to use an ecosystem-based approach, which considers the entire ecosystem rather than just specific issues. The NEP's management conference process was evaluated to see if it truly follows this approach. The assessment identified both strengths and weaknesses in how the NEP manages estuarine systems. Overall, adopting ecosystem-based approaches to environmental management could have significant implications for improving water quality and managing estuaries more effectively.