Graphene oxide (GO), a derivative of graphene consisting of various oxygen moieties, has gained popularity owing to its excellent physiochemical properties and applicability in various fields. GO nanomaterials can be synthesized by using Hofmann (HO), Hummers (HU), and Staudenmaier (ST) methods of oxidative treatment of graphite to give GO-HO, GO-HU, and GO-ST, respectively. These GO nanomaterials were found to exhibit different degrees of cytotoxicity that were suggested to be dependent on the amount and type of the oxygen-containing functional group present in the nanomaterials. Therefore, in this study, the transformations of GO-HO, GO-HU, and GO-ST nanomaterials in three types of natural waters over time were investigated to determine whether the oxygen-containing functional groups present in these nanomaterials undergo any changes after residing in natural waters. Based on the data obtained from Raman spectroscopy and X-ray photoelectron spectroscopy, although the density of defects in the GO nanomaterials remained relatively similar (a slight increase was detected in the GO-HO nanomaterials) over the period of examination, changes in the oxygen content of the GO nanomaterials were observed in most of the GO suspensions, which suggests that interaction between the natural waters and the GO nanomaterials do occur. Cyclic voltammetry measurements revealed that the natural waters had opposing effects on the GO nanomaterials: the GO-HU nanomaterials suffered a reduction in the amount of electroactive oxygen-containing functional groups present, whereas an increase was observed in the GO-HO and GO-ST nanomaterials. In addition, it was proposed that some of the electroactive oxygen moieties were completely lost from the GO-ST nanomaterials after exposing them to the natural waters. More studies should be performed in the future to comprehend the underlying mechanism for the transformations observed in this study so that the fate, transport, and toxicity of GO nanomaterials in environmental waters can be better understood.