- In response to increasing demand for aquaculture products and strict new regulations on organic matter and nitrogen discharge, inland closed recirculating aquaculture systems (RASs) are being developed as a viable eco-sustainable alternative to traditional aquaculture (e.g. ponds, raceways and cages) because of their minimal environmental impact and controlled operation. Fish feed is virtually the only source of carbon and nitrogen to the system. It is estimated that 20 to 30% of the feed nitrogen and 50% of the feed carbon are assimilated or utilized by the fish, while the rest is released to the water. Understanding the fate and utilization of these elements can help optimize RAS efficiency and economics. The fate of carbon and nitrogen was studied by mass balance in a novel near-zero discharge (< 1% water exchange of system's volume per day) saline research scale RAS. The system included a fish tank attached to three treatment loops: (a) a solid filter followed by an aerated nitrification fixed-film reactor, (b) a single-stage anoxic denitrification activated sludge bioreactor which utilizes fish sludge as a carbon source, and (c) an anaerobic bio-digester (upflow anaerobic sludge blanket [UASB]) for treatment of excess denitrification biomass for the production of biogas. About 50% of the introduced carbon (from feed) was removed by fish assimilation and respiration, and another 10% by aerobic biodegradation in the nitrification bioreactor. In the denitrification reactor, 10% carbon was removed and 25% carbon was introduced into the UASB reactor, of which 12.5% was converted to methane, 7.5% to CO2 and the rest (5%) remained as nondegradable carbon in the UASB. Using the UASB can save up to 12% of the system's energy demands, both directly as energy (methane) input and indirectly by reducing the system's oxygen demand. Of the feed nitrogen, 29% was assimilated by the fish and bacteria in the nitrification reactor and 40–50% was removed in the denitrification reactor, of which 10–20% was removed by anammox. Lastly, ~ 20% of the nitrogen was removed in the UASB reactor, likely by precipitation. It was demonstrated that the system was operating at high stocking density, with almost complete nitrogen and carbon removal and energy recovery. Statement of relevance The fate of carbon and nitrogen was studied by mass balance in a novel near-zero discharge (< 1%) saline RAS. A novel approach which may significantly reduce pollution, save water and energy and improve intensive aquaculture operations was demonstrated. It was postulated that the system operated at high efficiency, with almost complete nitrogen and carbon removal and energy recovery.