Photoelectrocatalytic (PEC) technology can be applied to treat ballast water. In this study, graphene oxide/zinc tungstate (GO/ZnWO4) electrodes were prepared to inactivate marine microorganisms. Results showed that microorganisms could be deactivated by GO/ZnWO4 electrodes under ultraviolet light and low-bias voltage. In particular, harmful microorganisms were deactivated by GO/ZnWO4 electrodes at 2 V bias in 8 min under ultraviolet light irradiation, and this duration was economically half the time of deactivation performed by ZnWO4 electrodes. GO plays a key role in electron and hole separation at a low voltage potential to avoid chlorine production by electrolyzing seawater at a high voltage in PEC. A hybrid heterojunction was also formed between GO and ZnWO4. This heterojunction increased the separation efficiency of electron-hole pairs, eliminated the hydrogen-related defect on the ZnWO4 surface, and improved the inactivation efficiency with a low applied potential. PEC could also elicit a synergistic effect with photocatalytic and electrocatalytic oxidation, which resulted in a high-separation efficiency of electron-hole pairs. This effect could also produce active substances, such as superoxide and hydroxyl radicals, and increase the inactivation efficiency of GO/ZnWO4 electrodes against harmful marine microorganisms. This work demonstrated that PEC is an efficient method to treat ballast water.