In this study, an up-flow zeolite media biological aerated filter (ZBAF) was developed and employed for the treatment of aquaculture wastewater. The results showed that ZBAF could start up quickly after 7 d and 25 d in viewpoint of mineralization and nitrification. 0.25 m/h and 20:1 were found to be the optimal hydraulic loading and gas/water ratio, under which around 85% of COD and 70% of NH4+ -N were removed stably in the ZBAF. Through analysis of water quality and microorganism along the flow direction, the heterotrophic and nitrifying population occupied respectively in the bottom and top of the filter column, and lower DO concentration was regarded as the boundary zone for these two different groups of chemotrophic bacteria. The changing profiles of biomass (phospholipid-P) and activity (oxygen uptake rate) showed the similar mode along the height of ZBAF, and their maximum values of 114.12 nmol/g and 0.67 mg/(g x h) were detected at the bottom of the filter.