Full-scale terminal disinfection of a commercial freshwater RAS using NaOH and H₂O₂: A Danish case study

Some fish farmers have implemented intensive cleaning and disinfection procedures encompassing entire production facilities. Despite the associated costs and production downtime, these strategies have reportedly improved subsequent fish performance and system functionality. This study documents a rigorous terminal disinfection procedure conducted at an open 1700 m 3 commercial freshwater rainbow trout recirculating aquaculture system (RAS). The treatment was performed during a production break after all fish had been removed and the system was bypassed circulating water without any discharge. Briefly, 2,000 L of 27% sodium hydroxide (NaOH) were added first, followed by 1,000 L of 35% hydrogen peroxide (H₂O₂) two days after. The system was then maintained under full recirculation for a total of three days. Water quality parameters were monitored throughout the disinfection period, and biofilter performance was assessed before, during, and after disinfection. Extreme water quality conditions were recorded, including pH values exceeding 11 for three consecutive days and circulating H₂O₂ concentrations above 100 mg/L. Hydrogen peroxide concentrations declined exponentially with a half-life of approximately–8 h and decreased to approximately 20 mg/L within 24 h after application. The disinfection procedure markedly altered microbial characteristics. The ratio of live to dead cells decreased from approximately 75:25 before disinfection to 7:93 during treatment, while total cell density increased from 3×10⁶ to nearly 2×10⁷ cells/mL. Nitrification was completely inhibited, resulting in prolonged accumulation of total ammonia nitrogen (TAN) and nitrite during system restart. Biofilter microbial activity was reduced by 91%, indicating that portions of the biofilm community survived the treatment. Because complete microbial elimination was not achieved, the findings emphasize the protective properties of biofilms and provide new insights into factors limiting terminal disinfection efficiency in RAS. The results further highlight the importance of mechanical cleaning and biofilm removal as components of effective sanitation protocols and demonstrate the need for quantitative methods to assess disinfection efficacy in aquaculture systems.