Regular monitoring of the microbiome in recirculated aquaculture systems will allow the farmer to link water quality parameters to subsequent fish performance and will function as a tool for early identification of microbial conditions that could lead to impaired fish health. Microbial communities were monitored in different compartments of a commercial full-scale, land-based saltwater RAS for production of Atlantic salmon during 9 months. The microbial communities revealed a unique composition in the production tanks and moving bed biofilters, as compared to the other investigated compartments. The fixed bed compartment had a higher stability in the microbial community over time, relative to the moving bed biofilter compartment. Changes of the operation of the facility (replenishment of brackish water to seawater) caused an immediate shift in the microbial populations. Potential geosmin producers (bacteria harbouring the functional gene for geosmin synthetase geoA) were dominated by Sorangium, Actinomycetales and Myxococcales, but unidentified microorganisms harbouring the geoA gene were also present. The biofilters had the highest numbers of potential geosmin producers, but their presence did not co-vary with the levels of geosmin. This suggest that an observed period with high levels geosmin were due to a change in activity, rather than an increase in cell numbers. Our results provide new insight into the diversity of microbiota in RAS and suggest that monitoring of microbial communities in the aquaculture production may provide a tool for future microbial management to ensure stability in RAS performance.