Formalin (a 33–38% aqueous formaldehyde solution) is currently used for bath treatments to control ectoparasitic infections of fish. Its effects on nitrification were evaluated in a semi-closed pilot scale saltwater recirculating turbot culture system. Tested treatments included 1 h static exposure to 20, 30, 40, 50, 60, 70, 90 mg l−1 formaldehyde without flushing, and long-term (i.e., 2, 4 and 6 h) exposures with constant 60 mg l−1 formaldehyde in a recirculating system. Formaldehyde has no apparent effect on the ammonia oxidative bacterial community. However, a significant effect on nitrite oxidation was observed in 1 h static exposures of concentrations higher than 40 mg l−1, and in recirculating system exposures of 60 mg l−1 formaldehyde for more than 4 h. Repeated treatments may be hazardous for nitrifying bacteria, which could induce an increase in nitrite concentration. Nitrite concentrations should be monitored when treatments are repeated or when they last a long time in recirculating aquaculture systems.