Pressurized expansive water seal is widely applied to weep holes of high head in water conservancy project. Due to many reasons, radial gate may suffer from leakage or even failure of the water seal and adapting pieces. Taking an actual project for example, most M20 stainless steel bolts on the bottom water clamping plate rotated out and were washed away in the first flood season after operation; in the second flood season, the bolts still fractured even after enlargement of the diameter of bolts (from M20 to M27) and improvement of bolts grade (from A2-70 to 10.9). In view of this, we investigated the hydraulic characteristics in the vicinity of the bottom water seal of the working radial gate via physical model test. Results unveiled that negative pressure and cavitation induced by high-velocity flow and resonance generated by flow-excited vibration are major causes of the failure of water seal system. Furthermore, through scheme optimization, we proposed an engineering countermeasure, which is to arrange baffle sill in the downstream reach near the slope of the gate slot. Test results demonstrated that flow condition in the exit segment has improved remarkably, negative pressure of water seal vanished, and flow cavitation number increased, implying evident energy dissipation and corrosion reduction effects. In addition, we recommend rigid connection instead of elastic connection between the clamping plate and the base plate in order to avoid resonance of the water seal system by keeping the natural frequency of the water seal system far from the dominant area of frequency distribution of fluctuating pressure. The research findings offer reference for the design and fault treatment of water seal system of radial gate.