A pilot-scale, two-stage (carbon oxidation stage one, ammonia oxidation stage two) fixed film biological aerated filter (BAF) process was operated on-site at a domestic wastewater treatment plant. Over the study period, hydraulic loadings to the system were varied, generating a range of organic and ammonia loading conditions. Nitrification was monitored along the length of the filters by measuring chemical nitrogen species and activity levels of ammonia oxidizing bacteria (AOB). During the first phase of the study, nitrification performance was characterized during the wintertime and compared with oligonucleotide probing results using an ammonia-oxidizer specific probe. Overall nitrification efficiency for wintertime conditions (average temperature 12.4 ± 0.1°C) was greater than 90 percent when ammonia-N loadings to the second stage were 0.6 kg/m3-day or less. Nitrification efficiency started to deteriorate at loadings beyond this point. Biofilm and liquid samples were collected along the distance of the two columns at high and low ammonia loadings. The degree of activity observed by ammonia oxidizing bacteria in the biofilm corresponded with the disappearance of ammonia and the generation of nitrate as water passed through the columns. During the second phase of the study, the probing methods were investigated and results of two approaches of analysis were compared to chemical nitrogen profiles. It was found that probe signals normalized to mass of total bacterial nucleic acid corresponded better with chemical profiles than using a novel method of standardizing against known nucleic acid mass standards. During both phases of the study, zones of ammonia oxidizing activity progressed along the length of the columns as organic and ammonia loadings to the system increased. The oligonucleotide probe data suggest that this shift in the location of the nitrifier population is due to higher BOD loads to the second stage, which supported higher levels of heterotrophic growth in the second stage of the system. It was concluded that the strongest influence on nitrification performance in this type of BAF system is likely to be competition between heterotrophs and autotrophs. / Master of Science