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The authors would like to thank the EU and the Spanish Government (AEI) (PCIN-2017-047) and Fundação para a Ciência e Tecnologia (FCT) (Water JPI/0003/2016) for funding, in the frame of the collaborative international Consortium AQUAVAL financed under the ERA-NET WaterWorks2015 Cofunded Call. This ERA-NET is an integral part of the 2016 Joint Activities developed by the Water Challenges for a Changing World Joint Programme Initiative (Water JPI) and the CDTI (Centro para Desarrollo Tecnológico Industrial, E.P.E., Spain). Authors also thank the Spanish Government (AEI) for funding, in the frame of the project TREASURE (CTQ2017-83225-C2-1-R) and the FCT for funding in the frame of the project UIDB/50016/2020. S. Santorio, A. Val del Rio and A. Mosquera-Corral belong to the Galician Competitive Research Groups (GRC)_ED431C-2021/37 co-funded by FEDER (UE) To avoid toxic ammonium and nitrite concentrations in aquaculture systems is crucial to maintain the fish production. When recirculating aquaculture systems (RAS) operate in freshwater farms during the dry seasons, the concentrations of these pollutants increase. The objective of the present study is the evaluation of a Continuous Flow Granular Reactor (CFGR) for the treatment of freshwater RAS stream at pilot-scale during two consecutive dry seasons. The CFGR was fed with a extremely low-strength recirculation stream of a trout farm (0.12–1.84 mg NH4+-N/L and 2.2–8.14 mg C/L). Two different configurations were evaluated. The first configuration consisted on a CFGR fed from the bottom, being the up-flow velocity the only shear force to mix the biomass. The second configuration incorporated a mechanical stirrer and a sieve to improve the biomass mixing and retention. The CFGR was operated at short hydraulic retention times (HRT) which ranged from 11 to 68 min. The configuration with a mechanical stirrer and sieve was optimal in terms of biomass retention and nitrogen removal performance. Despite the low nitrogen and organic matter concentrations, granulation was achieved in 55 days, with an average granule diameter up to 0.47 mm. Ammonium and nitrite removal percentages up to 81% and 100% were achieved, respectively. The ammonium and nitrite production rate in the trout farm were lower than the removal achieved by the CFGR, which makes the implementation of this system appropriated to maintain the concentration of these compounds below toxic levels for rainbow trout SI