Uranium (U) and Thorium (Th) are known to cause acute toxicological effects in human and their compounds are potential occupational carcinogens. During this work silica microsphere were used to decontaminate the traces of uranium and thorium in different water sources originated from groundwater and lake water. Ultra-filtration technique was used to isolate the microsphere from the water samples. Silica microspheres were synthesized based on a Polyvinylpyrrolidone (PVP) involved emulsion polymerization and subsequent sol-gel process. The microspheres were characterized for their size by using dynamic light scattering and presence of silicate structure is verified by recording their Attenuated Total Reflectanc -Fourier Transform Infrared spectrum (ATR-FTIR). The surface morphologies of the prepared silica microspheres were studied by using scanning electron microscope (SEM). Water samples collected from the groundwater and lake water were spiked with uranium and in the concentration range of 100 ng mL-1 to 1000 ng mL-1. The results of batch sorption experiments suggest that silica microsphere is very effective at pH 3 and sorption is more than 99.9%. Equilibrium sorption follows Langmuir isotherms and the maximum uranium and thorium uptake is 30 mg g-1 and 36 mg g-1 respectively. Major physiochemical characteristics of the water were monitored before and after the decontamination process. Experimental results show no significant variations in any of the measured parameters.