Composite Fenton nanocatalyst was prepared by water-based in situ creation of Fe3O4 nanoparticles integrated within the self-assembly 3D reduced graphene oxide (rGO) aerogel. The hybrid applied for the degradation of Acid Green 25 (AG-25) organic dye in an aqueous solution, in the presence of H2O2. By investigating the conditions that maximize the dye adsorption by the 3D composite, it was found that the pH of the solution should be adjusted between the pKa of the functional groups present on the rGO surface (carboxylic acid) and that of the dye (sulfonic acid) to promote electrostatic interactions dye-3D structure. Performed under these conditions, Fenton degradation of AG-25 in presence of H2O2 was completed in less than 30 min, including all the intermediate products, as demonstrated by MALDI-TOF-MS analysis of the aqueous solution after discoloration. Moreover, this was achieved in a solution with as high a dye concentration of 0.5 mg/mL, with only 10 mg of 3D composite catalyst, at room temperature and without additional energy input. The high performance was attributed to the creation of charge-transfer complex between rGO and Fe3O4 nanoparticles throughout covalent bond C-O-Fe, the formation of which was promoted by the in situ synthesis procedure. For the first time, up to the authors’ knowledge, AG-25 degradation mechanism was proposed.