CSO discharges have long been recognized as a significant source of water pollution. While many sources of water pollution have been controlled over the past 20 years, CSOs continue to be a main environmental concern in several areas, especially in old cities. In the past, most CSO research focused on the CSO control processes, including floatables and suspended solids removal. Few studies have been conducted in the area of the impacts of CSO discharge on the receiving water quality. To achieve this purpose, a powerful water-modeling tool, WASP 6.1, is utilized in this study. The Lower Hudson River is selected as a case study. Data are collected from the US EPA, USGS, NYC DEP, and NJ DEP. After calibration, the receiving water quality model can be used to study the impacts of CSO with a series of scenarios, which include the major factors that would affect the water quality of the receiving water. DO, BOD, ammonia, fecal coliform, and mercury are the reference pollutants discussed in this study. The simulation results are able to predict the effect of various CSO abatement alternatives on water quality and to be used in the water quality management and planning processes.