Competition between heterotrophic and nitrifying bacteria is of major practical importance in aquaculture biofilter design and operation. This competition must be understood to minimize the negative impact of heterotrophic bacteria on an aquaculture system. On the other hand, the heterotrophic population is suspected of having a positive effect against pathogenic bacteria. Little information is available on the bacterial communities present within aquaculture systems, except for nitrifying bacteria, but a combination of traditional aquacultural engineering research methods and novel microbiological techniques offers new opportunities for the study of these communities. The heterotrophic bacterial population activity and the nitrification efficiency of a submerged biological filter were studied for an influent TAN concentration of 2 mg/A and varying C/N ratios. The TAN removal rate was found to be 30% lower at a C/N ratio of 0.5 than at a C/N ratio of 0. For higher C/N ratios the reduction in nitfification efficiency was 50% while the attached bacterial abundance was doubled. Moreover, results confirm that abundance of sheared and attached bacteria are correlated. It is not known to what extent biofilter configuration might influence the relationship between heterotrophic and nitrifying bacteria, and further work will be carried out with moving bed and fluidized filters. A better understanding of the role of the heterotrophic bacteria in RAS will help to optimize any positive "biocontrol" effect and to minimize the microbial degradation of rearing water and the reduction of nitrification rates.