Several studies have employed rotating biological contactors (RBCs) for nitrogen removal. However, partially submersed disks are used for nitrification, while completely submersed disks are used for denitrification. The objective of this study was to investigate the effect of disk submergence in the performance of rotating biological contactors, in terms of the denitrification process. Two RBCs, one with completely submersed disks (100% submergence) and the other with partially submersed disks (64.5%), were operated under the same conditions. Their performance was evaluated in terms of denitrification efficiency as well as biofilm characteristics, composition and activity. As far as the denitrification process is concerned, the RBC with a completely submersed biofilm was more efficient than the other but had a longer delay in start-up. The biofilm of both reactors was very thick ( > 0.6 mm), but with different structures. Biofilm activity seems to be directly dependent on the biofilm structure, namely on the degree of hydration.