Globally water pollution has become a foremost issue that requires urgent attention requiring the application of innovative technologies to ensure a supply of clean water. Approximately 80 % of the world’s wastewater is released largely untreated back into the environment polluting water bodies. One of the main wastewater pollution sources is from the dyestuff industries which poses a serious threat to ecosystems due to the many adverse effects of dyes on human and environmental health. Conventional wastewater treatments are limited in terms of effectively treating such non-biodegradable contaminants; thus, there is an urgent need to develop new technologies that adequately treat such compounds. This work aimed to investigate the degradation of the commercial dye methylene blue (MB) using advanced oxidation processes (AOPs) using eco-friendly carbon-based nanoparticles as Fenton-like catalysts. Iron and nitrogen-containing carbon nanodots (Fe,N-CDs) were synthesised through a hydrothermal reaction and characterised using multiple physicochemical techniques including FTIR, XPS, TEM, ζ potential, PL and UV-Vis analyses. Moreover, dye degradation parameters were optimised by Taguchi method and evaluation of the effluent’s toxicity was assessed using Microtox® bioassay. Results showed that 7 nm diameter, negatively charged nanodots rich in iron and nitrogen surface functionalities were formed. Taguchi’s optimisation revealed that 50 °C, pH 8, H2O2 concentration of 147 mM and catalysts at 0.5 mg mL-1 were the optimum degradation parameters for removing nearly 100 % of MB in only 60 minutes. Notably, the ecotoxicological effects of the effluents treated with Fe,N-CDs were significantly decreased as assessed using Aliivibrio fischeri. This investigation showed that using Fe,N-CDs was an effective way to degrade wastewater pollution and significantly minimise its toxicity. Further work to investigate the efficiency of Fe,N-CDs on real environmental samples and their impact on aquatic biota are needed as these will help to elucidate the practical applicability of such technology.