Carbon-based nanomaterials (CNMs) have attracted a growing interest over the last decades. They have become a material commonly used in industry, consumer products, water purification, and medicine. Despite this, the safety and toxic properties of different types of CNMs are still debatable. Multiple studies in recent years highlight the toxicity of CNMs in relation to aquatic organisms, including bacteria, microalgae, bivalves, sea urchins, and other species. However, the aspects that have significant influence on the toxic properties of CNMs in the aquatic environment are often not considered in research works and require further study. In this work, we summarized the current knowledge of colloidal behavior, transformation, and biodegradation of different types of CNMs, including graphene and graphene-related materials, carbon nanotubes, fullerenes, and carbon quantum dots. The other part of this work represents an overview of the known mechanisms of CNMs’ biodegradation and discusses current research works relating to the biodegradation of CNMs in aquatic species. The knowledge about the biodegradation of nanomaterials will facilitate the development of the principals of “biodegradable-by-design” nanoparticles which have promising application in medicine as nano-carriers and represent lower toxicity and risks for living species and the environment.