The microbial consortium of a moving bed bioreactor (MBB) connected to a marine recirculating aquaculture system was examined by denaturing gradient gel electrophoresis (DGGE) of amplified 16S rRNA gene fragments. Both ammonia and nitrite oxidizers, Nitrosomonas cryotolerans and Nitrospira marina, respectively, were found associated with the marine system as well as a number of heterotrophic bacteria, including Pseudomonas sp. and Sphingomonas sp. In addition, two Planctomycetes sp. were detected in the system suggesting the capability for anaerobic ammonia oxidation (anammox). The potential for carrying out different nitrogen transformation processes—nitrification, denitrification and anammox—by the bead consortium in both low and high organic load MBBs was measured by short-term batch incubation. Beads with a high organic load exhibited a lower nitrification rate (25 mg NH3–N/m2/h) than low organic load beads (31.5 mg NH3–N/m2/h) as well as the ability to carry out denitrification and anammox processes. The potential of using MBBs to induce different nitrogen transformation processes was evaluated, and it was found that this type of bioreactor has the capability to serve as a platform for mediating desired anoxic processes such as denitrification and anammox.