The most perilous environmental hazards arise from the contamination of water by heavy metal ions, owing to the non-biodegradability of these metals, as well as their rapid dissemination throughout components of the environment via the food chain. Nano-based adsorbents have been used for the adsorption removal of many heavy metal cations, but separating and recycling them represent significant difficulties in processing. Magnetic core–double shell nanoparticles provide an attractive solution for processing issues, since they are stable and can be easily separated and recycled. Moreover, the shell thickness, composition, and porosity can be easily tuned. In this work, two samples consisting of magnetic core@TiO2@mesoSiO2 nanoparticles with two shell thicknesses (Mag-T-S-0.2 and Mag-T-S-0.4), along with a magnetic core@SiO2@TiO2 nanoparticle sample (Mag-S-T), were synthesized and characterized by TEM, XRD, magnetic strength measurement and zeta potential. TEM images show the developed core–double shell structure with double shell ranging from 60 to 73 nm. The XRD results indicate the impact of the outer shell on the diffraction pattern. The zeta potential shows that all samples had a negative charge at pH over 4. The magnetic character was suppressed after the formation of the double-shell coating; however, the magnetic core–double shell nanoparticles still had magnetization and could be separated when an external magnetic field was applied. The heavy metal adsorptive ability of Mag-T-S-0.2, Mag-T-S-0.4, and Mag-S-T samples was explored to investigate the effects of shell type and thickness along with kinetic, isotherm, and thermodynamic study. The investigated heavy metals included Cd(II), Ni(II), Mn(II), Pb(II), and Cu(II). The results indicate that, for Mag-T-S-0.2, the equilibrium state occurred after 15 min contact time, with adsorption capacity of 238, 230, 210.6, 181.8, and 245.8 mg/g for Cd(II), Ni(II), Mn(II), Pb(II), and Cu(II), respectively. For Mag-T-S-0.4, the equilibrium state occurred after 15 min contact time, with adsorption capacity of 241, 237.6, 173.8, 189.6, and 257.2 mg g−1, respectively. For Mag-S-T, the equilibrium state occurred after 25 min contact time, with adsorption capacity of 137.8, 131.4, 221, 189.6, and 149.4 mg g−1, respectively. When pseudo-first-order and pseudo-second-order kinetic models were applied to investigate the time interval adsorption data for Mag-T-S-0.2, Mag-T-S-0.4, and Mag-S-T samples, the second-order kinetic model was found to be more suitable for describing the process, indicating a fast adsorption mechanism. The adsorption data did not fit well with the Langmuir model, while they did fit well with the Freundlich model, suggesting heterogeneous material surfaces and multi-layer adsorption. Thermodynamic investigations confirmed the spontaneous nature of adsorptive removal, which helps to promote magnetic core@TiO2@mesoSiO2 and magnetic core@SiO2@TiO2 nanoparticles as effective adsorbents for wastewater treatment.