The increased discharge of water pollutants drives the development of new and effective wastewater remediation methods. Herein, a magnetic nanocomposite of chitosan-graphene oxide (GO) decorated with copper ferrite (MCSGO) was synthesized under ultrasound agitation and applied to the effective removal of Safranin O (SAF) and indigo carmine (IC) dyes from wastewater. The structural, magnetic, and physicochemical features of the as-prepared MCSGO nanocomposite have been thoroughly investigated using various characterization techniques. The operational parameters such as MCSGO mass, contact time, pH, and initial dye concentration were investigated. The effects of diverse coexisting species on both dye elimination processes were examined. The experimental results demonstrated that the adsorption capacity of MCSGO nanocomposite for IC and SAF was 112.6 and 66.15 mg g⁻¹, respectively. Five different adsorption isotherms were investigated using two-parameter (Langmuir, Tekman, and Freundlich) and three-parameter (Sips, and Redlich–Peterson) models. Thermodynamic studies revealed that the elimination of both dyes on MCSGO nanocomposite was endothermic and spontaneous, with anionic and cationic dye molecules randomly arranged onto the adsorbent nanoparticles. Moreover, the mechanism of dye elimination was deduced. Furthermore, even after five cycles of adsorption and desorption, the as-prepared nanocomposite showed no significant loss in the dye removal efficiency, indicating that it has superior stability and recycling potential.