Underwater arc discharge is one of the most effective water treatment methods because of the effects of intense shockwaves and high ultraviolet radiations. In this paper, a high-voltage underwater arc discharge system is proposed to study the inactivation of <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Escherichia coli</i> bacteria, which has an arc-robust feature. It consists of a high-voltage capacitor charger and a discharge circuit. The high-voltage capacitor charger is developed by an LCCL resonant converter to reach a current supply scheme that is inherently protected and robust against arc discharge. The detailed mathematical analysis and the design optimization of the resonant converter are presented. The discharge circuit is developed by a two-step spark gap scheme using an ultrafast highvoltage trigger circuit, providing a reliable system operation independent of the water conductivity. The proposed underwater arc discharge system is applied to 500ml of pollutant water to study the system’s performance on the inactivation of <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">E. Coli</i> bacteria. The proper microbiological tests are carried out, showing the effectiveness of the proposed underwater arc discharge system. The complete inactivation of <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">E. Coli</i> bacteria is achieved in an extremely short treatment time. Moreover, the experimental results are presented, which validate the desired performance of the proposed underwater arc discharge system.