The Chicago Waterways System (CWS) is very complex and a complete understanding of the flow and water quality phenomena is not possible with current modeling tools. Among many interesting aspects, bi-directional flows have been observed in the Main Branch of Chicago River (MBCR) during winter time. Instead of flowing downstream into the South Branch (SB), part of the water from North Branch (NB), which usually carries runoff from a 100 square mile watershed and treated municipal sewage effluent released by the North Side Water Reclamation Plan (WRP), might flows into MBCR. This will have a huge impact on the water quality in MBCR, where the downtown Chicago is located. Physical model and field measurements of the CWS have been done to investigate the possible cause. Through these previous studies, density current has been identified as one of the main cause. A preliminary three dimensional numerical model also has been used in University of Illinois at Urbana and Champaign (UIUC) to simulate the density current. Although the bi-directional flow phenomena have been reproduced in the 3D model, the flow conditions are simplified and only very short period of time is simulated. In this paper, a three-dimensional environmental fluid dynamics code (EFDC) is used to simulate the flow in the Chicago River system (including NB, SB, and MBCR). EFDC is a public domain code which is supported by the Environmental Protection Agency (EPA) and has been widely used in many rivers and estuaries. It uses stretched or sigma vertical coordinate and Cartesian or curvilinear, orthogonal horizontal coordinate. Three-dimensional, hydrostatic, free surface, and turbulent flow equations are solved. Water quality models (such as sediment, temperature, toxics, dissolved oxygen, and biological oxygen demand) are also implemented. For this paper, the EFDC code is modified to simulate only the density current in CWS mainly due to the dissolved particles. The tests cases used in this paper are from the physical model work done in the hydrosystems lab in UIUC. The numerical model is validated and tested against the experiments. Good results have been achieved. More numerical simulations will be done to expand the parameter space. Water quality models will be activated in the future to see the environmental impact of different management strategies.