Abstract Particle accumulation in recirculating aquaculture systems (RAS) are generated from uneaten food and feces, and bacteria tends to proliferate. Small organic particles act as substrate for bacterial growth and may by direct interference with gills cause stress and reduce disease resistance for the cultivated species. Most diseases in aquaculture of marine fish larvae are caused by opportunistic microorganisms that become pathogenic when the fish is under stressed conditions. The present study investigated the potential of using a membrane bioreactor (MBR) as a part of the water treatment in a RAS for production of marine fish larvae, since the small pore size (50 nm) efficiently removes organic particles including the colloidal fraction in the system. The experiment was a 50 day start-feeding experiment with Atlantic cod ( Gadus morhua L.), comparing water quality and larval performance in a conventional RAS (cRAS) with a membrane filtrated RAS (mRAS). In mRAS, 8.5% of the water flow was at any time membrane filtrated. The present study showed that the MBR improved water quality significantly by reducing turbidity and by lowering the total number of bacteria in the rearing water (up to 80% reduction). Microbial communities in water samples were significantly different between cRAS and mRAS already on 5 days post-hatching (dph) and throughout the experiment. The microbial community composition of the rearing water was significantly different from the composition of the larval microbiota during the experiment, although differences between larval samples were different only on 50 dph. The present study showed the potential of using MBR to lower the bacterial carrying capacity (CC) by efficiently removing organic particles and bacteria. In average a 13% higher cod larval growth (weight, %) at 40 dph and a 3.0% higher survival rate at 50 dph were measured in the mRAS scheme.