The Lake Champlain Basin in Vermont and New York, USA and Quebec, Canada includes a large lake and watershed with complex management issues. A transboundary comprehensive management plan prepared for the lake includes 11 goals across many issue areas. We developed a choice experiment to examine public preferences for alternative Lake Champlain management scenarios across these issue areas. Five ecosystem attributes (water clarity-algae blooms, public beach closures, land use change, fish consumption advisories and the spread of water chestnut, an invasive plant) were varied across three levels and arrayed into paired comparisons following an orthogonal fractional factorial design. Two thousand questionnaires were distributed to basin residents, each including nine paired comparisons that required trading off two, three or four attributes. Completed surveys yielded 6541 responses which were analyzed using binary logistic regression. The results showed that although water clarity and beach closures were important, safe fish consumption was the strongest predictor of choice. Land use pattern and water chestnut distribution were weaker but also significant predictors, with respondents preferring less land development and preservation of the agricultural landscape. Current management efforts in the Lake Champlain Basin are heavily weighted toward improving water clarity by reducing phosphorus pollution. Our results suggest that safe fish consumption warrants additional management attention. Because choice experiments provide information that is much richer than the simple categorical judgments more commonly used in surveys, they can provide managers with information about tradeoffs that could be used to enhance public support and maximize the social benefits of an ecosystem management program.