The accumulation of nitrate in closed marine systems presents a problem for both the marine life and the environment. The present study, proposes the application of the ion exchange membrane bioreactor (IEMB) concept for removing nitrate from marine systems, such as aquaculture tanks or marine aquariums. The results obtained demonstrate that the IEMB was able to remove naturally accumulated nitrate from water taken from a public marine aquarium (Oceanário de Lisboa) and bioconvert it, in an isolated compartment (biocompartment), to molecular nitrogen, thus preventing secondary contamination of the treated water by microbial cells, metabolic by-products and excess of carbon source (ethanol). This system allowed for the removal of nitrate at concentrations of 251 and 380 mg/l down to below 27 mg/l exchanging it for chloride. Under the studied operating conditions, the IEMB proves to be a selective nitrate removing technology preserving the initial water composition with respect to cations, due to the Donnan exclusion effect from the membrane, and minimizing the counter diffusion of anions other than nitrate and chloride, due to the use of water with the same ionic composition in the biocompartment. This is an advantage of the IEMB concept, since the quality of the water produced would allow for the reutilisation of the treated water in the aquarium, thereby reducing both the wastewater volume and the use of fresh water.