Bubbly Creek was historically used as a drainage channel for the waste resulting from Chicago's stockyards. Nowadays there is flow in the creek only during rainfall events resulting in Combined Sewer Overflows (CSO) and water quality is a very important issue, particularly during the summer months, when the dissolved oxygen levels are extremely low and sediment oxygen demand is expected to be large. Due to the particular flow regimes of the creek and the conditions of the benthic sediments in the bed, a special BOD-DO (Biochemical Oxygen Demand - Dissolved Oxygen) water quality module was developed and implemented into the two-dimensional depth-averaged numerical model STREMR-HySedWq. The approach illustrated represents a substantial improvement to the state-of-the-art of water quality modeling methodologies. The model was able to capture the key processes and provide useful preliminary results for the two following scenarios:  CSO events, for which the model was coupled to a one-dimensional cross-section-averaged BOD-DO water quality model, and  potential "purification" solutions, such as flow augmentation and supplemental aeration, with the goal of increasing the DO levels in the creek during dry weather periods.