Carbon-based materials (CBM), including activated carbon (AC), activated fibres (ACF), biochar (BC), nanotubes (CNT), carbon xenogels (CX) and graphene nanosheets (GNS), possess unique properties such as high surface area, sorption and catalytic characteristics, making them very versatile for many applications in environmental remediation. They are powerful redox mediators (RM) in anaerobic processes, accelerating the rates and extending the level of the reduction of pollutants and, consequently, affecting positively the global efficiency of their partial or total removal. The extraordinary conductive properties of CBM, and the possibility of tailoring their surface to address specific pollutants, make them promising as catalysts in the treatment of effluents containing diverse pollutants. CBM can be combined with magnetic nanoparticles (MNM) assembling catalytic and magnetic properties in a single composite (C@MNM), allowing their recovery and reuse after the treatment process. Furthermore, these composites have demonstrated extraordinary catalytic properties. Evaluation of the toxicological and environmental impact of direct and indirect exposure to nanomaterials is an important issue that must be considered when nanomaterials are applied. Though the chemical composition, size and physical characteristics may contribute to toxicological effects, the potential toxic impact of using CBM is not completely clear and is not always assessed. This review gives an overview of the current research on the application of CBM and C@MNM in bioremediation and on the possible environmental impact and toxicity.