Recirculating aquaculture systems (RAS) are good candidates for the sustainable development of the aquaculture sector. A current limitation of RAS is the production and accumulation of nitrogenous waste, which could affect fish health. We investigated the potential of the anaerobic ammonia oxidation (anammox) process to treat marine wastewater from a cold-water RAS. We show that the marine anammox bacteria Candidatus Scalindua is a promising candidate. However, its activity was affected by unknown compounds in the RAS wastewater and/or the sub-optimum of essential trace elements (TEs). Anammox activity dropped to 2% and 13% in NH4+ and NO2- removal, respectively, when nitrate-rich RAS wastewater was used as a medium in the absence of TE supplementation. A TE supplementation was added to the RAS wastewater in a subsequent phase, and a recovery in anammox activity was shown (25% and 24% in NH4+ and NO2- removal, respectively). Future studies need to identify the unknown factor and determine the specific needs regarding TE for optimal RAS wastewater treatment by Candidatus Scalindua.