The valorisation of oil palm empty fruit bunch is challenging due to its poor surface functionalities, which require a comprehensive pre-treatment process. To ensure efficient valorisation of the agricultural waste, the biochar derived from empty fruit bunch is subjected to hydrothermal nitric acid pre-treatment to act as an adsorbent for sodium ions removal from the saline solution. For this newly developed adsorbent, the adsorption study provides important information on the adsorption behaviour of sodium ions and the optimum conditions for sodium ions removal, which is crucial for effective process design and operation control during practical applications. Physicochemical characterisation revealed the successful adsorption of sodium ions by Hydrothermal Nitric acid Pre-treated EFB Biochar (HNO3 EFB-BC. The highest sodium ions removal efficiency of HNO3 EFB-BC (92.04%) was achieved under the optimum reaction conditions: 0.39 M initial concentration of the saline solution, 4.96 g of HNO3 EFB-BC, contact time of 17.4 h and solution pH of 7.46. Upon process optimisation, the adsorption capacity of HNO3 EFB-BC towards sodium ions improved remarkably (p < 0.05) from 78.34 mg g-1 to 166.45 mg g-1. The adsorption isotherm and kinetic study are consistent with the Langmuir and pseudo-second-order models, implying a monolayer chemisorption-dominated adsorption process. The promising sodium ions adsorption capacity of HNO3 EFB-BC can be attributed to the enhanced surface functionalities of the adsorbent. The molecular modelling using the density functional theory approach has successfully identified the nitro group as the most favourable functional group in producing the charges sites for sodium ions adsorption, with the most stable reaction route between HNO3 EFB-BC and sodium ions being identified. This study highlighted the density functional theory approach as a tool for identifying the specific functional groups with enhanced adsorption capability for saline water treatment and provides a reference value for removing sodium ions in the presence of other cationic pollutants.