Over the course of ten years, a consortium of stakeholders (the Harbor Consortium) used a collaborative approach to identify viable pollution prevention (P2) strategies for specific contaminants, namely mercury, cadmium, polychlorinated biphenyls (PCBs), dioxins, and polycyclic aromatic hydrocarbons (PAHs) as well as suspended solids entering the New York/New Jersey Harbor. The project, titled “The New York/New Jersey Harbor Watershed Pollution Prevention and Industrial Ecology Project,” in a very conscious and overt way engaged stakeholders in the process of developing P2 recommendations for the Harbor. The industrial ecology (IE) tools applied by the Harbor Consortium include substance flow analysis (SFA), material flow analysis (MFA), and, to a limited extent, life cycle analysis (LCA) and fate and transport analysis (F&T), to quantify and characterize how the contaminants flow through the regional economy and the Harbor Watershed once released to the environment. The application of these scientific tools to five contaminants at such a large geographical scale, within the context of a broad and inclusive stakeholder process, and with the goal of identifying and implementing pollution prevention strategies, led to a wide range of surprising outcomes and lessons learned. Undertaking this IE research with the key institutions and stakeholders at the table resulted in the identification and the implementation of many P2 opportunities.