We propose a new optical biosensor based on a SiO2/Si photonic crystal with a defect layer, which can determine the concentration of SARS-CoV-2 in water by the defect mode shift. Two models of the dependence of the refractive index of the defect layer on the concentration of the pathogen in water were considered. The optimal parameters of the photonic crystal in our device were determined such as the thickness of the SiO2 and Si layers of the ideal photonic crystal of 0.720 and 0.275 μm, respectively, and the optimal thickness of the defect layer of 1.87 μm was also determined. It was also demonstrated that in the presence of absorption in the structure under study, it is much more advantageous to operate in the reflection mode compared to the transmission mode. Finally, the wavelength dependence of the defect mode on the SARS-CoV-2 concentration was obtained and the sensitivity of the sensor was determined to be 1020 nm/RIU.