Three bench-scale nutrient removal activated sludge units were used to examine the effect of the reactor configuration and the intermittent aeration mode on the growth of Microthrix parvicella. According to the results, the plug flow configuration seems to achieve satisfactory Microthrix parvicella control. The imposed concentration gradient for both RBCOD and SBCOD creates a selective advantage for the floc forming bacteria throughout the system (both the anoxic and oxic zones) and limits Microthrix parvicella growth. In terms of the operational mode, the intermittent aeration CSTR nutrient removal system promotes the growth of M. parvicella and deteriorates the settling characteristics of the activated sludge.