Due to the unique chemical and physical properties, graphene-based nanomaterials are increasingly being introduced into various scientific fields. They all play very important roles in different fields and are widely used. Graphene oxide (GO) is one of the most popular and representative carbon nanomaterials; scientists have great research interest in it. When carbon nanomaterials such as GO are released into the aquatic environment, their physicochemical properties will be influenced by natural light, resulting in the potential change in toxic effects on aquatic organisms. Algae, as a typical aquatic organism, is extensively regarded as a model microorganism to assess the biotoxicity of nanomaterials. In this review, we overview the light-mediated impact of GO on algae. We summarize the photo-transformation of GO under different illumination conditions and the effect of illumination on the physicochemical properties of GO. Then, we combined metabolomics, genotoxicity, and proteomics with standard toxicity assays (cell division, membrane permeability, oxidative stress, photosynthesis, cellular ultrastructure, and so on) to compare native and environmentally transformed GO induction toxicological mechanisms. By correlating lights, physicochemical properties, and biotoxicity, this review is valuable for environmental fate assessments on graphene-based nanoparticles, providing a theoretical basis and support for evaluating the potential ecological health and environmental risks of graphene-based nanoparticles in real natural water environments.