AbstractBubbly Creek is the historical name given to the West Fork of the South Branch of the Chicago River (SBCR). Even though its base flow is small, during extreme storm events Bubbly Creek becomes an important tributary to the Chicago Area Waterway System (CAWS). During extreme storm events, combined sewer overflows (CSOs) discharged by the Racine Avenue pumping station (RAPS), located at the head of the creek, can result in large flow velocities, potentially entraining into suspension bottom sediments, which contain abundant organic muck and buried waste. Under normal storm flow conditions, the flow discharge from Bubbly Creek flows first into the SBCR and then is conveyed by the Chicago Sanitary and Ship Canal (CSSC) towards Lockport, Illinois. However, during extreme rainfall events the conveyance capacity of the CSSC is exceeded, so there is a flow reversal, and Bubbly Creek water and sediments flow north, along the SBCR and then towards Lake Michigan via the Chicago River controlling works (CRCW). Due to lack of field observations during storms, the entrainment, transport, and fate of sediments from Bubbly Creek during reversed-flow conditions, cannot be easily assessed. This motivated the use of numerical modeling to evaluate the erosion, transport, and deposition of sediments from Bubbly Creek on the CAWS. The public-domain three-dimesional (3D) environmental fluid dynamics code (EFDC) was used to simulate hydrodynamics and sediment transport for two storm events with normal and reversed flow directions and high CSO discharge. Results show that RAPS discharge picks up sediment from Bubbly Creek, causing high-suspended sediment concentrations due to high rates of bottom material resuspension. In the September 2008 storm, approximately 8% the sediment reached CRCW and went into Lake Michigan during flow reversal, while 83% of the sediment went south along the CSSC towards Lockport, Illinois. Herein, the novelty is in shedding light on applying a 3D cohesive sediment module to evaluate the erosion, transport, and fate of organic muck and cohesive sediments originating in Bubbly Creek along the CAWS. The flow and sediment partitioning, bed morphology, and its potential impact on the system could be analyzed under normal and reversed flow conditions for both recently deposited as well as legacy sediments accumulating since RAPS went into operation almost a century ago. Capping of legacy sediments together with periodic dredging of sediments deposited after a CSO event could be an alternative worthwhile considering for urban streams like Bubbly Creek, where flow only takes place after extreme rainfall events.