The aim of this work was to quantify the activity of autotrophic and heterotrophic populations present in a submerged membrane bioreactor submitted to a sequenced aeration, ensuring alternate nitrification and denitrification (BIOSEP(R) process). Specific nitrification and denitrification rates Were determined over a fifteen-month running period, with, and without physico-chemical phosphorus removal. The results show (i) zero-order kinetics; (ii) a specific activity independent of MLVSS concentration; and (iii) an evolution of the nitrification kinetics directly linked to an evolution of the nitrifying population within the unit. The study confirmed that denitrification kinetics, depend on the concentration and on the nature of wastewater organic matter.