In Recirculating Aquaculture Systems (RAS) various chemical compounds (mainly nitrates and organic carbon) accumulate in the rearing water. These chemical substrata regulate the ecophysiology of the bacterial communities of the biofilter and have an impact on its nitrification efficiency and reliability. In the present study chemical and microbiological parameters in static mineral bed (SBB) and moving plastic bed (MBB) biological filters were monitored at increasing C/N ratios ranging from 0 (pure nitrification) to 4 (combined nitrification and organic carbon removal), with the aim to investigate the shift of the bacterial community structure and major taxa relative abundances. Results suggest that the MBB are less subjected to the nitrification reduction than the SBB, probably due to their self-cleaning characteristic. Moreover, the dynamics and flexibility of the bacterial community to adapt to influent water changes seemed to be linked with the biofilter performance. The increase of the C/N ratio resulted in a shift of the bacterial community structure in term of reduction of taxa richness and diversity indices, and in a positive selection of the Gammaproteobacteria (especially in the SBB). One of the key aspects for improving the reliability and sustainability of RASs is a proper management of the biofilter bacterial populations, which is directly linked to the C availability. Nevertheless, it is a pertinent question whether it is possible to modify the composition of a microbial community in an environment like a biological filter, using direct microbe controlling systems (e.g. water exchange, UV disinfection, etc.).