A large sewer overflow tunnel was designed to store excess runoff during large storm events. After the storm event the tunnel is slowly drained and treated. During the time between the storm and draining the tunnel, debris settles on the bottom of the channel. After draining the tunnel, a storage tank upstream releases a large flow to flush the storage line. Typical network modeling tools were inadequate to evaluate the transient flushing flow condition. HEC-RAS was used in an innovative way to evaluate the flushing flow in the tunnel and solve this problem. HEC-RAS typically models open channel flows and can be used to efficiently simulate transient flow events. Because the flushing flow would propagate through the tunnel completely as a gravity flow, HEC-RAS was seen as an appropriate tool to investigate the transient flow. A combination of two tunnel cross sections and 3 flushing volumes were evaluated. HEC-RAS was able to predict the scour time available in each section of the tunnel. This analysis successfully determined the appropriate tunnel bottom configuration and required flushing volume.