One of the principal factors in Shale instability is the stress variation due to water invasion into Shale in water-based drilling fluids, consequently causes in wellbore instability. This comprehensive study aims to improve the rheological properties and plug the nanometers Shale pore throat with biogenic silica oxide Nanoparticles. To do this, a new procedure of waste product from an agricultural industrial named Rice husks (RHs), amorphous silica oxide (SiO2) Nanoparticles (NPs) with a purity of 97.7% synthesized. Due to extracted from natural materials, amorphous silica has unique properties that do not exist in its crystalline state. One of these points is environmentally friendly than crystalline shape, which belongs to the first group of carcinogens for humans. The NPs characterization was performed by Field Emission Scanning Electron Microscope (FESEM), Energy-dispersive spectroscopy (EDS), X-Ray Fluorescence (XRF), Transmission electron microscopy (TEM). The utilization of synthesized NPs in the water-based drilling fluid at two concentrations of 3 and 5% w/v illustrated that the mud-based rheological properties such as viscosity and fluid loss were improved. Pore Pressure Transmission (PPT) apparatus is applied to investigate the effect of the synthesized NPs to plug Shale pore throats. The PPT test results showed that 3% w/v of NPs block the pore throats of interlayer Shale of Asmari Formation and reduce the rate of fluid penetration in Shale is about 5.6%. Moreover, at the concentration of 5% w/v NPs, fluid invasion into Shale reduces up to 43.7% compared to base mud. Consequently, synthesized NPs from RHs could be used as an efficient method to improve the rheological properties of water-based muds and stabilize the Shale layer.