Baffled Biological Aerated filter (BBAF) is an innovative biofilter for wastewater treatment. The arm of this work is to investigate the variation of pollutants concentration and microorganism population along the depth of media. Removal efficiency of organic pollutants and ammonia along the media depth of baffled biological aerobic filter were measured. Quantity of heterotrophic bacteria and nitrobacteria in representative depth of media was examined with MPN test, and microorganism population of each filter was studied by means of microscopic observation. The characteristics of microorganism population distribution in BBAF was studied by means of microscopic observation. The results show that COD concentration decreases gradually with the increase depth of media layer. The front four filters have good performance on organic pollutants removal, but performance on ammonia removal is weak, indicating that heterotrophic bacteria is dominating microorganism in these filters. In conditions of lower organic loads bring about a higher growth of nitrobacteria increases the nitrification efficiency in filter five to filter seven. Because the existence of concentration gradient in different filters of BBAF, dominant microorganism population might be formed along the depth of filter media layer and favored the improving treatment efficiency of BBAF.