We develop a theory that explains the decrease in saturated hydraulic conductivity Ks due to biological clogging of porous media. Experiments show that discontinuous microcolonies in fine-textured soils decrease Ks more severely than biofilms do. However, most existing models for biological clogging assume that bacteria cells form biofilms which uniformly cover pore walls. We propose a mathematical model for biological clogging with a quantitative evaluation of the nonuniform microbial distribution of colonies. A series of equations describing the relation between the biological clogging and the saturated hydraulic conductivity are derived. The data of previous researchers are used to validate the model. ¿ 2001 American Geophysical Union