The pollution profiles of Nakivubo channel and wetland, and the spatial distribution of ammonium‐oxidizing bacteria and the corresponding ammonium‐oxidation activities along Nakivubo channel and wetland are presented. A set of physico‐chemical and biochemical variables was monitored, and numbers and activity of ammonium‐oxidizing bacteria in the water, sediment and epiphyton were quantified to estimate their influence on the nitrification and nitrogen bioconversions in general, and to determine the factors influencing the distribution of ammonium‐oxidizing bacteria in Nakivubo channel and wetland. Considerable numbers of ammonium‐oxidizing bacteria and ammonium‐oxidation activities were found upstream of Nakivubo channel suggesting that the physico‐chemical conditions were suitable for the survival of nitrifying bacteria. However, the longitudinal decline in numbers and activity of ammonium‐oxidizers was probably due to (1) high biodegradable organic matter input which supported proliferation of heterotrophs, consuming the little available oxygen, (2) hydro‐sedimentary conditions of the channel, (3) die‐off due to presence of toxic and inhibitory chemicals and metal compounds. The removal of biochemical oxygen demand was significantly higher than that of nitrogen indicating lower self‐purification efficiency for nitrogen. A comparison of the ammonium‐oxidation activity of the different phases indicated that epiphytic nitrification was more important than that of sediment and water compartments of the wetland, whereas sediment and suspended nitrifiers were equally important for nitrification upstream of Nakivubo channel.