This work analyzes the discharge characteristics of water plasma for a miniature microwave discharge ion thruster via three-dimensional particle-in-cell simulations with Monte Carlo collisions. It incorporates the negative ions (H−, O−, and OH−) into the simulation code, aside from the three major positive ion species (H2O+, OH+, and H+), and investigates their effects on the discharge characteristics. On the one hand, the simulation results indicate that H2O+ is the dominant species and the negative ions have little effect on the positive ion density and transport. On the other hand, this study confirms the axial oscillation of the OH− negative ion density, in addition to azimuthal rotation, causing plasma instability with a periodic low-frequency anomalous diffusion. The azimuthal rotation is similar to the phenomena observed in other E × B devices, where the difference in spatial distributions of magnetized electrons and unmagnetized ions causes the local potential hump and the resultant instability. Moreover, the axial oscillation, not observed in the previous study considering only positive ions, is due to the generation of OH− by the charge transfer collision reaction between H2O and H−, and this oscillation frequency is double that of the azimuthal rotation. Both the azimuthal rotation and the axial oscillation result in the periodic double peaks of the potential time evolution. These fluctuations have an influence on electron transport across the magnetic field.This work analyzes the discharge characteristics of water plasma for a miniature microwave discharge ion thruster via three-dimensional particle-in-cell simulations with Monte Carlo collisions. It incorporates the negative ions (H−, O−, and OH−) into the simulation code, aside from the three major positive ion species (H2O+, OH+, and H+), and investigates their effects on the discharge characteristics. On the one hand, the simulation results indicate that H2O+ is the dominant species and the negative ions have little effect on the positive ion density and transport. On the other hand, this study confirms the axial oscillation of the OH− negative ion density, in addition to azimuthal rotation, causing plasma instability with a periodic low-frequency anomalous diffusion. The azimuthal rotation is similar to the phenomena observed in other E × B devices, where the difference in spatial distributions of magnetized electrons and unmagnetized ions causes the local potential hump and the resultant instability. M...