This chapter provides a comprehensive overview of current research on carbon-based nanomaterials (CNMs) in aquatic organisms, focusing on their occurrence, behavior, and ecotoxicity. It delves into the synthesis and unique properties of key CNMs, such as graphene, carbon nanotubes (CNTs), fullerenes, carbon nanofibers (CNFs), and amorphous carbon, highlighting their significant applications and the environmental concerns associated with their increasing use. The chapter discusses the potential sources of CNMs in aquatic environments, including industrial emissions, consumer products, and degradation processes. It explores the analytical methods used to detect and quantify these materials. It addresses the complex interactions between CNMs and natural organic matter (NOM), which can influence their behavior and toxicity, and examines the various transformation processes CNMs undergo in aquatic systems. The ecotoxicological impacts of CNMs on different aquatic organisms, from microalgae to fish and turtles, are thoroughly reviewed, with detailed examples from recent studies illustrating acute and chronic effects. The chapter also identifies key limitations in current research, such as the lack of standardized methodologies and comprehensive toxicokinetic data. It emphasizes the need for integrated, multidisciplinary approaches to understand better and mitigate the risks posed by CNMs. Finally, it highlights future research directions, including developing standardized testing protocols, investigating long-term and multigenerational effects, and applying emerging technologies like synthetic biology and computational nanotoxicology. The chapter underscores the importance of translating scientific knowledge into effective regulatory policies to protect aquatic ecosystems from the potential adverse impacts of CNMs.