Legionella pneumophila were previously identified in the aeration ponds (up to 10(10) CFU/L) of a biological wastewater treatment plant at Borregaard Ind. Ltd., Sarpsborg, Norway, and in air samples (up to 3300 CFU/m(3)) collected above the aeration ponds. After 3 outbreaks of Legionnaires' disease reported in this area in 2005 and 2008, the aeration ponds of the plant were shut down by the Norwegian authorities in September 2008. The aim of the present work was to analyze the Legionella and non-Legionella bacterial communities in the aeration ponds before and during the shutdown process and to identify potential human pathogens. The non-Legionella bacterial community was investigated in selected samples during the shutdown process by 16S rDNA sequencing of clone libraries (400 clones) and growth analysis. The concentration of L. pneumophila and Pseudomonas spp. DNA were monitored by quantitative PCR. Results showed a decrease in the concentration of L. pneumophila and Pseudomonas spp. during the shutdown. This was accompanied by a significant change in the composition of the bacterial community in the aeration ponds. This study demonstrated that several advanced analytical methods are necessary to characterize the bacterial population in complex environments, such as the industrial aeration ponds.