Abstract Water failures, which can be diagnosed with alternating-current impedance, is harmful to output properties and durability of the proton exchange membrane fuel cell. In this paper, an impedance-based measuring method of the zero-phase ohmic resistance is presented, which adjusts the measuring frequency to confine the impedance point within the ±3° sampling limitation area so as to guarantee the accuracy of 0.01 mΩ. The zero-phase ohmic resistance is sensitive to the membrane dehydration, and it decreases in the flooding process due to the gradual liquid water accumulation in the catalyst layer. The fluctuation of the zero-phase ohmic resistance increases in the flooding process, owing to the water state variation resulting from increasingly frequent water removal. A semi-empirical equivalent circuit model is used to analyze the change of mass transfer in the flooding process, and it is found that the diffusion resistance and the dissolution resistance of the reactant increase sharply. The fixed-low-frequency resistance is applicable in the flooding diagnosis, whose sensitivity changes with the chosen frequency. The highest sensitivity is corresponding to the peak value of the impedance magnitude. This paper provides adequate information about the water fault diagnosis, making sense to the fault-avoidance and the durability-promotion of the fuel cell.