Continued mortality from Covid‐19 disease and environmental considerations resulting from the cemetery, landfill, wastewater treatment plants, and mass personal protective equipment (PPE) disposal sites demonstrate the importance of carefully studying how microorganisms spread in and across the soil, surface water, and groundwater. In this research, fractional diffusion equation for different functions has been solved using fractional derivative form with variable‐order (VO) to predict the diffusion of the SARS‐CoV‐2 virus. Comparison of the obtained results with the available experimental data and mathematical calculations shows that the use of VO form can predict the viral behavior more accurately. The main advantage of considering a VO fractional derivatives instead of a constant‐order fractional derivative or classical derivative is accurately predicting the behavior of propagation of microorganisms over large time and dimensional scales. In addition, to the specified SARS‐CoV‐2 virus, the method presented in this study will be able to investigate the diffusion pattern of all environmental pollutants at the nanoscale/microscale, including carcinogenic compounds, such as biogenic amines in aqueous and porous media. The obtained results manifest a high accuracy of mathematical approach which provides helpful information to urban and health planners/managers worldwide to manage other possible outbreaks.