Currently, there have been a major concern for water pollution causing by rapid expand of human activities. The nitrate contamination in receiving water is one of the cause for eutrophication and public health concern. This study was focused on the nitrate accumulation within the recirculating aquaculture system by using the combination of natural zeolite and denitrifying bacteria culture. The ion exchange between zeolite and various ions including nitrate ion was due to the chemical structure of zeolite.The use of zeolite at the concentration of 150 g/l within 2 hour was found to give the highest nitrate removal (42%). The presence of denitrifying bacteria assisted the denitrification process when being added carbon source (methanol). The overall nitrate removal efficiency was obtained up to 97% by the selected condition.