Deep storage tunnels (DSTs) are used in densely urbanized areas to relieve stormwater collection systems, thereby reducing urban floods and runoff pollution, due to their substantial storage capacity. The computation of the hydraulic characteristics and flow trajectories of DSTs under rapid filling scenarios can help to predict sediment deposition and pollutant accumulation associated with the stored runoff, as well as the likelihood of operational problems, such as excessive surging. However, such assessments are complicated by various inflow scenarios encountered in tunnel systems during their operation. In this study, the Suzhou River DST in China is selected as a study case. Particles were tracked, and hydraulic analysis was conducted with scaled model experiments and numerical models. The flow field, particle movement, air‒water phase, and pressure patterns in the DST were simulated under various one- and two-sided inflow scenarios. The results showed that with regards to the design conditions involving two-sided inflows, flow reversals occurred with stepwise increases in the water surface and pressure. In contrast, this phenomenon was not observed under the one-sided inflow scenario. Under the asymmetric two-sided inflow scenarios, water inflows led to particle accumulation near the shaft, reducing the received inflows. However, under the symmetric inflow conditions, particles were concentrated near the middle of the tunnel. Compared to those under the symmetric inflow scenario, asymmetric inflow caused surface wave and entrapped air reductions. This study could provide support for regulation of the inflow of the Suzhou River DST and for prediction of sediment and pollutant accumulation.