We studied the role of scientists and scientific information in the decision-making processes used by local jurisdictions and communities in San Mateo and Santa Clara Counties, California, to address a contentious environmental dispute involving flooding and habitat restoration of the San Francisquito Creek. Although a great number of scientific studies have been undertaken and continue to be commissioned, the parties have not used the results to help resolve the dispute. We conclude that the absence of an effective collaborative process, which is based on consensus seeking strategies, is a major reason why science is not effectively used and why the communities cannot reach agreement on a solution to the dispute. In this regard, we studied the growing demand for greater public participation, as contrasted to traditional public involvement, in science-related policy making and in decision-making in general. We suggest that Joint Fact Finding as a component of a comprehensive consensus building and participatory decision-making process is a better approach for incorporating science into environmental policy making. Joint Fact Finding enables the active participation of citizens as partners with governmental representatives in framing the questions that address the issues and in designing and implementing the studies. This process maintains the independence of the scientists and their commitment to the best science. A well-designed Joint Fact Finding process will improve the capacity of all participants to learn from all forms of knowledge and to reach resolution of contentious environmental disputes.