A predictive method of microbial clogging assessment was presented on the basis of the microorganism growth theory and the quality relationship between the amount of biofilm and hydraulic conductivity of porous media. Furthermore, we applied this method to evaluate potential microbial clogging degree of the recharge water in Pinggu. The results have shown that clogging occurs within the upper 0.5 m near the land surface with a permeability reduction of only 2.3%.