Transient flow events can potentially damage infrastructure and threaten public safety in the vicinity of violent flow eruptions that occur where tunnel drop shafts interconnect with the surface-combined sewer system. Transient events have been observed in tunnels and at drop shafts in the tunnel and reservoir plan (TARP) system in Chicago on a number of occasions since operations first began in 1985. For the most part, the phenomenon has been controlled effectively by operating the system in a conservative mode through controlling the rate of filling. Nevertheless, more recently, not only water transients but also geysering events—the intermittent discharge of a combination of water and air from a hydraulic system—have occurred at the terminus of branch tunnels where controlled filling is not effective. The Metropolitan Water Reclamation District of Greater Chicago (MWRDGC), the operating agency for the system, has been prompted to develop engineering solutions to minimize transient flow occurrence and negative effects at the affected drop shaft locations. To this end, numerical modeling was conducted to investigate the cause and potential solutions. Such modeling included one-dimensional (1D) hydraulic transient modeling of a large domain in the system, followed by more detailed three-dimensional (3D) two-phase flow simulations within a smaller domain. The 1D approach revealed the interaction between localized events of interest and other transient flow features that originate far from the drop shaft under consideration. Computational fluid dynamics (CFD) modeling results show the complex interaction of trapped air and water in the tunnels. Even though more field observations are needed to test the accuracy of model predictions, careful interpretation of the results made it possible to pinpoint the problem and propose a solution. The findings also provided insight into the importance of considering both inertial instabilities as well as air–water interactions in geysering mechanics.