In aquaria and rearing tanks, nitrate accumulation as a result of organic matter degradation is inevitable and has two major negative side effects: direct toxicity to organisms, specially invertebrates, and the introduction of a reducing environment by oxygen consumption. The aim of this study was to compare two alternate methods of removing nitrogen compounds from closed systems, autotrophic columnar denitrification (ACD) and heterotrophic columnar denitrification (HCD) by following end product concentrations as reaction progressed. A pilot plant consisting of two series of 50 dm 3 recirculating flow systems (each in triplicate) was used to test both methods. Absence of pH control was also useful in autotrophic denitrification systems in order to follow effects over reaction rates and pathways. Concentrations of NO 3 - , NO 2 - and NH 4 + were followed throughout the experiment, as well as pH, temperature and salinity. Under different flow conditions results show that higher nitrate reduction rates were possible in the autotrophic systems (35.1+/-4.7 μM/day without pH control until reversal of the process and 20.6+/-7.3μM/day after reestablishment of pH control) in comparison with heterotrophic (9.9+/-1.3μM/day). However, pH control through calcium bicarbonate addition was found to be crucial in maintaining constant levels of total denitrification in ACD systems, just as it was necessary to closely maintain organic carbon addition to HCD systems.