This work developed a Schiff base-chitosan-vanillin/hydroxyapatite (CHI-VAN/HA) composite from natural resources for effective brilliant green (BG) dye removal from aquatic systems. Physicochemical analysis of CHI-VAN/HA was performed via several methods, including BET, XRD, FTIR, and SEM-EDX. The mean pore diameter and total pore volume of CHI-VAN/HA were found to be 4.31 nm and 0.01994 cm3/g, respectively, while the BET surface area was found to be 18.49 m2/g. The CHI-VAN/HA composite mostly exhibits polycrystalline properties, as shown by its average crystallite size of 12.67 nm. Box-Behnken design (BBD) in response surface methodology (RSM) was used to optimize the impacts of the adsorption process parameters, namely the CHI-VAN/HA dosage (A: 0.02-0.08 g/L), pH (B: 4-10), and contact duration (C: 10-40 min). The adsorption process was described using the Freundlich isotherm and pseudo-first-order kinetic models. The thermodynamic analysis confirms that the adsorption process is both spontaneous (Gibbs free energy change, ΔG° = -6.832, -7.368, -7.904, and - 8.440 kJ/mol at 298, 308, 318, and 328 K respectively) and endothermic (enthalpy change, ΔH° = 9.156 kJ/mol), with increased interfacial disorder (entropy change, ΔS° = 0.0536 kJ/molK) facilitating the favorable uptake of BG dye onto the CHI-VAN/HA composite. The cost analysis for preparing 1 kg of CHI-VAN/HA adsorbent is approximately $215/kg. The CHI-VAN/HA composite exhibited a maximum adsorption capacity of 295.74 mg/g for BG dye. Several interactions, including electrostatic, π-π, n-π, H-bonding, and Lewis acid-base interaction, were identified as the mechanism for the BG dye adsorption. This work highlights that the developed Schiff base-chitosan-vanillin/hydroxyapatite composite, derived from natural sources, offers an eco-friendly and sustainable solution for brilliant green dye removal. Its excellent adsorption performance and physicochemical properties underscore its potential application in wastewater treatment and environmental remediation.