In this research study a nitrifying/autotrophic denitrifying system was used for the post-treatment of an effluent coming from an anaerobic digester treating the wastewater produced in a fish canning industry. The nitrifying reactor achieved 100% of ammonia oxidation into nitrate. The effluent from this unit was fed to the autotrophic denitrifying reactor which treated a maximum sulphide loading rate (SLR) of 200 mg S-2-/L d with removal percentages of 100% and 30% for sulphide and nitrate, respectively. The low nitrate removal efficiency is attributed to sulphide limitations. The operational costs of this system were estimated as 0.92 (sic)/kg N-removed, lower than those for conventional nitrification/denitrification processes. For nitrogen removal the SHARON/anammox processes is the cheapest option. However the combination of nitrification and autotrophic denitrification (using elemental sulphur) processes would present a better operational stability compared to the SHARON/anammox system. Crown Copyright (C) 2013 Published by Elsevier Ltd. All rights reserved.