The long-term project on the survey of filamentous microorganisms, which started in 1996, was finished in 2000 by the survey of eight Czech activated sludge plants with biological nutrient removal (BNR) systems. At all plants with enhanced biological nutrient removal, specific microbial population (mostly from the point of view of filaments occurrence), operational problems (presence of biological foaming, bulking) and plant operation were observed periodically and longer than 1 year. In our paper the relationship between the composition of activated sludge (especially filaments) consortia and modification of the process with nutrient removal is discussed. At the surveyed plants Type 0092 and Microthrix parvicella were identified as dominant Eikelboom filamentous types.