Clogging in intermittent sand filter (ISF) systems was analyzed using an unsaturated flow model coupled with a reactive transport model. Based on the results of a model sensitivity analysis, several variables were determined to be important in the clogging phenomena observed in ISFs, including hydraulic loading rate, influent chemical oxygen demand (COD) concentration, filter dosing frequency, and time of operation. Several modes of operation were identified that minimize the growth of bacteria at the filter surface. Following the sensitivity analysis, several case studies where ISF clogging was documented were simulated using the model. The results from the case study model simulations were found to be correlated with the total suspended solids loading rate (TSSLR) at the point of clogging. A model was developed that relates biomass development at the surface of ISFs with the TSSLR that can be sustained without clogging. The engineering significance of the model is presented in terms of operational and design considerations.