Deep wastewater treatment is carried out by a bioconveyer technology and a direct-flow system of multistage biological treatment (DSMBT). To reduce excess biomass and energy costs, the first bioreactors (sections) of the DSMBT provide for partial removal of soluble organics in the absence of oxygen, the rest are intended for aerobic water treatment. Development of a method for engineering calculation of anaerobic biofiltration as applied to the first sections of DSMBT is the main aim of the study. Anaerobic substrate utilization is modeled at two levels using two stage biokinetics. The behavior of the substrate and its derivatives within a representative biofilm are analyzed, taking into account surface and molecular diffusion, limitation of the rates of the substrate and acid biodegradation, coexistence of two communities of microorganisms. The behavior of the original and newly formed organic substrates in the volume of a representative section is studied by analytical methods. A theoretical base and an engineering method for calculating anaerobic biofiltration are developed and illustrated, which can serve as the basis for applied optimization of the parameters of bioconveyer plants. It is justified to use the derived calculation dependencies for similar complex biological treatment plants with any filtering material.