Nowadays the World is facing a scarcity of safe drinking water and the water sector encounters great challenges. The impact of a growing population and the change of climate on water availability and quality; public health and environmental issues related to emerging pollutants are the major challenges that need to be addressed. In drinking water, there may be a chance of having water-related diseases and health issues due to the occurrence of some pathogens. In the present study, we synthesized nanosilica from rice husk and it was encapsulated with sodium alginate beads and tested its efficiency for removal of bacteria from drinking water. These beads are novel since it is fully bio-origin, biodegradable and cost-effective. The isolated nanosilica were characterized spectroscopically and morphologically (FT-IR, XRD, FESEM, and HRTEM). The synthesized beads were characterized by FT-IR, FESEM, and EDX and antibacterial analysis. Using the Petrifilm method and column disinfection experiment, different filler loadings were optimized and found that higher content (1.25 g) of nanosilica reduced bacterial contamination of drinking water. The alginate-nanosilica beads are cost-effective compared to alginate beads incorporated with other nanomaterials. The antibacterial evaluation verified superior antibacterial efficacy against E.coli. The prepared alginate-nanosilica beads can be used in the wastewater treatment industry, as an effective antibacterial agent.