Though scientists agree that eutrophication is a key driver of HABs in Lake Erie, the role of nitrogen is still the subject of debate. The problem is twofold: (1) uncertainty in the specific causes of HABs can lead to inappropriate management solutions, and (2) managing a cross-boundary watershed requires collaboration and agreement on apt solutions from multiple stakeholders as well as many U.S. states and Canadian provinces. In our study, we interviewed 29 stakeholders actively involved in western Lake Erie’s watershed. We analyzed the stakeholders’ values, attitudes, and policy preferences to understand their differences, similarities, and their effects on management decisions. We found that stakeholders agree on the urgency of the problem and the necessity for increased nutrient management in Lake Erie’s western basin. Furthermore, we found that stakeholders can be represented as distinct clusters based on their values, and these value-based clusters are associated with different policy preferences. The different opinions and preferences of these value clusters span across stakeholder sectors and may affect efforts toward policy change. Stakeholders often question the feasibility and effectiveness of existing policies and policy plans. The findings shed new light on the relationship between stakeholder type and environmental values, attitudes, and policy preferences. Collaboration on HABs in Lake Erie will require open lines of communication both to improve policy and to cultivate trust among the multiple parties in this diverse watershed.