An up-flow biological anoxic filter (BANF) has been developed to achieve high removal performance of suspended solids and BOD removal as well as nitrogen. With a view to understand treatment mechanisms, we developed a filtration model that incorporates filtration, deposit scoring and biological reactions simultaneously. The biological reactions consist of four types of reaction; dissolution of organic particles; utilization of dissolved organic matter; denitrification; and self-degradation of bacteria. Whereas the reactor is generally assumed to be a plug flow reactor in the filtration model, it is assumed a continuous-flow stirred tank reactor (CSTR) in the model of biological reactions. The hydrodynamics is supposed that the filter bottom (the portion sludge settled) is a CSTR and the filter bed (the portion filled with filter media) consists of number of CSTR of equal size arranged in series. The model obtained in this study was verified and simulated using experimental results taken from a pilot-scale plant and predicted the experimental data well, applying to design and operate BANF.