Graphene oxide (GO) is widely employed due to its outstanding properties, leading to an increasing release into the environment and natural waters. Although some studies have reported on the photo-transformation of GO, its behavior in complex natural waters remains inadequately explored. This study demonstrates that different types of ions may promote the photoreduction of GO in the order of Ca2+ > K+ > NO3− > Na+ by interacting with the functional groups on the surface of GO, and the photoreduction is enhanced with increasing ion concentrations. Additionally, natural organic matter (NOM) can inhibit the photoreduction of GO by scavenging reactive oxygen species. However, with increasing NOM concentrations (≥ 5 mgC/L), more NOM adsorb onto the surface of GO through hydrogen bonding, Lewis acid-base interactions, and π-π interactions, thereby enhancing the photoreduction of GO. On this basis, our results further indicate that the combined effects of different ions, such as Ca2+, Mg2+, NOM, and other complex hydrochemical conditions in different natural waters can promote the photoreduction of GO, resulting in a reduction in oxygen functional groups and the formation of defects. This study provides a theoretical basis for assessing the long-term transformation and fate of GO in natural waters.