The Harlem River, a 9.3-mile channel that flows from the Hudson River to the East River, has experienced decades of industrial abuse and remains gritty and industrial. During heavy rains, the pipes discharge raw sewage into the river through combined sewer overflows (CSOs) that can contain bacteria and cause illness. Water samples were collected from CSO discharge point and several adjacent sites along the river in the Bronx side close to River Park Towers at Richman Plaza and Manhattan side at Wards Island. Nutrients, bacteria, polychlorinated biphenyls (PCBs), and fish consumption safety have been analyzed. Results showed that phosphorus, ammonia concentration as well as fecal coliform, E.Coli, enterococcus levels increased significantly during heavy rainstorms. Ammonia concentration was up to 2.725 mg/L during tropical storm Arthur on C 12 H 8 C l2 ), the high molecular weight (MW), an indicator of raw sewer and storm water runoff in the NYC harbor waters, is the major polychlorinated biphenyls (PCBs) in the Harlem River. PCBs are carcinogenic, which could bioaccumulate via food chain from fish and seafood, endangering public health. Oyster farming has been used to purify water and improve water quality in the river. CSOs and storm water runoff have degraded water quality and been threatening environmental ecosystem and public health. This research will help local communities understand CSO impact on nutrients, bacteria, PCBs contamination and fish consumption safety, and make contributions on CSOs reduction as well as improve water quality and environmental ecosystem in the Harlem River.