In this work, calcium silicate/sodium calcium silicate nanostructures were facilely produced by sol–gel method. The sol–gel process involves the transformation of a colloidal solution into a gel and then further processing the gel to form a solid material. After that, the produced nanostructures were functionalized with chitosan and chitosan/glutaraldehyde as novel nanocomposites. In addition, the produced nanostructures and their corresponding nanocomposites were employed for the effective sorption of Cd(II) and Cu(II) ions from aqueous solutions by ion exchange and complexation processes. The maximum adsorption capacity of the produced nanostructures, nanostructures/chitosan, and nanostructures/chitosan/glutaraldehyde samples towards Cd(II) ions is 166.94, 236.97, and 324.68 mg/g, respectively. Besides, the maximum adsorption capacity of the same samples towards Cu(II) ions is 202.84, 287.36, and 348.43 mg/g, respectively. The adsorption of Cd(II) and Cu(II) ions was chemical, spontaneous, exothermic, and best described by the pseudo-second-order kinetic model and the Langmuir equilibrium isotherm. The study found that 9 M HCl effectively removed Cd(II) or Cu(II) ions from the synthesized adsorbents, achieving a desorption efficiency exceeding 99%. Furthermore, the produced adsorbents demonstrated excellent reusability over five consecutive adsorption/desorption cycles for the sorption of Cd(II) and Cu(II) ions.