In this study, a CoO–Fe2O3/SiO2/TiO2 (CIST) nanocomposite was synthesized and utilized as an adsorbent to remove methylene blue (MB), malachite green (MG), and copper (Cu) from aqueous environments. The synthesized nanocomposite was characterized using field emission scanning electron microscopy (FE-SEM), Fourier-transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), and X-ray diffraction (XRD). Input parameters included pH (3–10), contact time (10–30 min), adsorbent amount (0.01–0.03 g), and pollutant concentration (20–60 mg L−1). The effects of these parameters on the removal process efficiency were modeled and optimized using the response surface methodology (RSM) based on the Box–Behnken design (BBD). The RSM-BBD method demonstrated the capability to develop a second-degree polynomial model with high validity (R2 ˃ 0.99) for the removal process. The optimization results using the RSM-BBD method revealed a removal efficiency of 98.01%, 93.06%, and 88.26% for MB, MG, and Cu, respectively, under optimal conditions. These conditions were a pH of 6, contact time of 10 min, adsorbent amount of 0.025 g, and concentration of 20 mg L−1. The synthesized adsorbent was recovered through five consecutive adsorption–desorption cycles using hydrochloric acid. The results showed an approximately 12% reduction from the first to the seventh cycle. Also, MB, MG, and Cu removal from real water samples in optimal conditions was achieved in the range of 81.69–98.18%. This study demonstrates the potential use of CIST nanocomposite as an accessible and reusable option for removing MB, MG, and Cu pollutants from aquatic environments.