The mechanism of significant nitrogen loss in an aerobic rotating biological contactor (RBC) treating ammonium-rich waste water could be identified with the aid of batch experiments, mathematical modeling and microbial analysis. It turned out that the aerobic ammonium and nitrite-oxidizing organisms (nitrosomonas and nitrobacter clusters) are dominant in the upper aerobic 100-200 μm of the biofilm. It is assumed that nitrite, appearing as an intermediate product close to the surface of the aerobic biofilm layer, diffuses into deeper anoxic layers of the biofilm. It is reduced anaerobically there in parallel with ammonium oxidized as described in the Anammox (anaerobic ammonium oxidation) process. This was confirmed in an anoxic batch test with suspended biofilm removed from the RBC. Unknown micro-organisms were detected, some of them similar to the Anammox organisms. A mathematical model which describes the kinetics of the aerobic ammonium-oxidizing, aerobic nitrite-oxidizing and anoxic ammonium-oxidizing micro-organisms was formulated and fitted into the AQUASIM biofilm compartment. The distribution of the populations within the biofilm as well as the ammonium, nitrite and nitrate degradation along the RBC in a steady state and during short-term experiments were modeled and compared with the experimental data.