Due to the wide range of water levels in reservoir operation, the hydraulic functionality of free surface tunnels in supercritical flow conditions, while discharging beyond design conditions, deserve further studies. To investigate the safe discharging of low drop tunnels, a scale model of a spillway system was built and tested under different flow conditions and structural configurations. Water depth, velocity and flow regime in tunnel and flip bucket reach were measured in experiments. In emptying reservoir operations, a surprising phenomenon was observed; specifically, at low discharges, supercritical flow occurred inside the tunnel while subcritical flow characterized the exit section, with a hydraulic jump forming and moving back into tunnel, forcing it to work under pressure. Critical discharge conditions below which hydraulic jump occurs in the tunnel is theoretically derived by 1D hydraulic analytical computation and experimentally confirmed as q(c) =0.485q(d). To eliminate risk of choked tunnel, a modification is envisioned by setting a torsion angle and a side-weir along the flip bucket section. Experiment results indicate that the combination of a skewed flip bucket and side weir can effectively decrease the outlet water depth, and mitigate the hydraulic jump, avoiding tunnel choking thanks to redirecting the flow into the side weir and to centrifugal force effects. Ski jump flow through the skewed flip bucket and the downstream river regime were also improved.