The aim of this study was to synthesize novel and highly efficient functionalized material (BNMPTS) for selective elimination of Cu2+ and Cd2+ from aqueous waste. The detailed insights of solid/solution interactions were investigated by X-Ray photoelectron spectroscopic analyses. The grafting of silane caused for significant decrease in specific surface area of bentonite from 41.14 to 4.65 m2/g. The functionalized material possessed significantly high sorption capacity (12.59 mg/g for Cu2+ and 13.19 mg/g for Cd2+) and selectivity for these cations. The material showed very high elimination efficiency at a wide range of pH ~2.0 to 7.0 for Cu2+, ~3.0 to 10.0 for Cd2+ and concentration (1.0 to 25.0 mg/L) for Cu2+ and Cd2+. A rapid uptake of these two cations achieved an apparent equilibrium within 60 minutes of contact. The increased level of background electrolyte concentrations (0.0001 to 0.1 mol/L) did not affect the elimination efficiency of these two cations by BNMPTS. Moreover, the common coexisting ions did not inhibit the removal of these toxic ions. Furthermore, high breakthrough volumes i.e., 1.4 and 3.69 L for Cu2+, 2.6 and 6.64 L for Cd2+ was obtained using 0.25 and 0.50 g of BNMPTS respectively in a fixed-bed column operations.