Water management is an important issue for proton exchange membrane fuel cells (PEMFC). The research mainly focuses on the diagnosis and treatment of faults. However, faults harm PEMFC and cause its durability decay, whatever duration they last. This study designs a closed-loop water management system to control the water content in a reasonable range which can not only avoid the faults of hydration and flooding but also improve the performance and durability of PEMFC. The proposed system introduces the measurement methodology based on the phase of single-frequency impedance, which corresponds numerically well with the water content. Moreover, two preferred operating conditions, cathode air stoichiometry and stack temperature, are adopted to regulate the water content with a trade-off between the time cost and power loss. The open-loop characteristics of water content on the temperature and air stoichiometry are studied to design the corresponding control strategy. Findings suggest that air stoichiometry is suitable for large regulation requirements of water content, while the temperature is suitable to meet small demands. Finally, the proposed closed-loop water management system is validated by experiments in variable-load and constant-load with disturbance situations. The results indicate that the proposed system effectively controls the water content within a 3% deviation from the desired value.