In this work, the water quality status of the surface water that lies around the Karamana River basin, Trivandrum urban area, was studied on the basis of the water quality index (WQI) method. The eutrophic condition of the basin is revealed, and proper mitigation strategy was adopted for the removal of phosphate species using pillared clay materials. Proper sampling was carried out in the urban rivers, and various physico-chemical parameters for evaluating the quality of water were analysed. WQI values obtained for these riverine systems are in the range 317.7–3005.1, indicating that the water is not suitable without treatment for any domestic activities. Also, phosphate ions in the range 1.98–20.52 mg/L reflect the dominance of phosphate species in surface water. A proper mitigation strategy was adopted for the selective removal of phosphate ions using adsorption technique by using zirconium-pillared bentonite clay (ZPBC) prepared by the stirring–ageing technique. The batch adsorption experiment performed on simulated phosphate solution shows that for 2.0 g/L of ZPBC a maximum phosphate adsorption capacity of 35.71 mg/g was achieved in 30 min at pH 3.0. The data obtained were used to study models in kinetics and isotherm. The reusability of spent ZPBC for five continuous cycles without major loss in adsorption capacity using 0.025 M Na₂CO₃ extractant was proved from the desorption study. A single-stage reactor was also designed from the isotherm data and proved to be effective. The applicability of the adsorbent towards phosphate anions was successfully checked in the laboratory using surface water collected and found that the complete removal of phosphate was achieved using 6.0, 8.0 and 10.0 g/L of ZPBC.