Chitosan (Cs)-based composites were developed by incorporating silica (Cs–Si), and both silica and hydroxyapatite (Cs–Si–Hap), comparatively tested to sequester hexavalent (Cr(VI)) ions from water. XRD and FT-IR data affirmed the formation of Cs–Si and Cs–Si–Hap composite. Morphological images exhibits homogeneous Cs–Si surface, decorated with SiO2 nanoparticles, while the Cs–Si–Hap surface was non-homogeneous with microstructures, having SiO2 and Hap nanoparticles. Thermal analysis data revealed excellent thermal stability of the developed composites. Significant influence of pH, adsorbent dose, contact time, temperature, and coexisting anions on Cr(VI) adsorption onto composites was observed. Maximum Cr(VI) uptakes on Cs and developed composites were observed at pH 3. The equilibration time for Cr(VI) adsorption on Cs–Si–Hap was 10 min, comparatively better than Cs and Cs–Si. The adsorption data was fitted to pseudo-second-order kinetic and Langmuir isotherm models with respective maximum monolayer adsorption capacities (qm) of 55.5, 64.4, and 212.8 mg/g for Cs, Cs–Si, and Cs–Si–Hap. Regeneration studies showed that composites could be used for three consecutive cycles without losing their adsorption potential.