The nanochitosan/clinoptilolite (Nano-CS/Clino) composite, Nano-CS/Clino activated by hydrochloric acid (Nano-CS/[email protected]) and Nano-CS/Clino functionalization with pentaethylenehexamine (Nano-CS/[email protected]) has been used to removal of nitrate ions from aqueous media. The textural properties of the Nano-CS/Clino nanocomposites were studied by various characterization techniques. The Nano-CS was synthesized by ionic gelation technique that using tripolyphosphate as cross-linking agent. The BET specific surface area of chitosan and Nano-CS is 0.9774 and 52.8850 m²/g. The effects of different parameters on the removal of nitrate were measured in detail. The prepared Nano-CS/[email protected] composite possess enhanced nitrate adsorption capacity of 277.77 mg/g than Nano-CS/[email protected] and Nano-CS/Clino were found to be 227.27 and 185.18 mg/g. The Dubinin–Radushkevich, Freundlich and Langmuir adsorption models were applied to describe the equilibrium isotherms. The experimental data were also analyzed by first- and second-order and intra particle diffusion. Thermodynamic parameters studies revealed that the nature of adsorption nitrate by nanocomposites synthesized is spontaneous and exothermic. The overall adsorption tendency of synthesized nanocomposites toward nitrate (NO₃⁻) in the presence of CO₃²⁻, SO₄²⁻ and Cl⁻ under competitive conditions, followed the order: NO₃⁻ > CO₃²⁻> Cl⁻> SO₄²⁻. Desorption process was carried out with NaOH and proven it was an effective agent in the discharge of nitrate.