Abstract The New York/New Jersey Harbor (also known as the Hudson River Estuary) is heavily contaminated with polychlorinated biphenyls (PCBs) arising in part from inputs from the Upper Hudson River, which is a Superfund site containing historical PCB contamination, and also due to inputs from the New York City metropolitan area. The Contamination Assessment and Reduction Project (CARP) measured PCBs and other contaminants in ambient water samples collected throughout the Harbor region during 1998–2001. In order to investigate the sources of PCBs to the NY/NJ Harbor, this data base of PCB concentrations was analyzed using Positive Matrix Factorization (PMF). This analysis resolved seven factors that are thought to be associated with sources such as the Upper Hudson River, storm water runoff, combined sewer overflows (CSOs), and wastewater effluents. The PMF model also produced a factor that appears to be related to sites contaminated with Aroclor 1260. To the extent that the NY/NJ Harbor is typical of urbanized estuaries throughout the United States, these results suggest that storm water runoff is probably a significant source of PCBs to surface waters in urban areas.