A pilot-scale, two-stage (carbon oxidation stage one, ammonia oxidation stage two) fixed film biological aerated filter (BAF) process was operated during the wintertime on-site at a domestic wastewater treatment plant. Over the study period, hydraulic loadings to the system were varied and generated a range of organic and ammonia loading conditions. Nitrification performance was monitored based on water quality along the length of the filters, effluent water quality, and activity levels of ammonia-oxidizing bacteria within the biofilm using an oligonucleotide 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. The 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 column.