The Chicago Area Waterway System (CAWS) includes the Chicago Sanitary and Ship Canal (CSSC) and the Calumet-Sag Channel (Cal-Sag), the two primary, man-made connections between the Mississippi River Basin and the Great Lakes. The U.S. Geological Survey (USGS) monitors diversion of Great Lakes water at a streamgage just downstream of the confluence of the CSSC and Cal-Sag (known as Sag Junction). Previous studies have explored the complex hydrodynamics in the CAWS near Sag Junction and at the USGS streamgage near Lemont, Illinois. The current study explores the mixing at Sag Junction which can be purely advection-driven or driven by density differences between the two branches. The current study simulates and analyzes two cases: 1) the density of water in CSSC is greater than in the Cal-Sag, 2) the density of the CSSC water is less than in the Cal-Sag. The density difference between the branches was found to play a major role in influencing the mixing process compared with purely advection-driven mixing. Density differences created near-bed gravity currents, some of which intruded upstream into the CSSC or Cal-Sag creating bi-directional flows. The phenomenon of double plunging was observed, along with formation of a recirculation zone between the two plunging fronts. Local mixing at the confluence was enhanced by density differences between the two channels, but mixing downstream from the confluence was impeded due to formation of a stabilizing stratification.