Florfenicol (Aquaflor®) is the only U.S. Food and Drug Administration (FDA) approved drug for treating diseased fish reared in recirculating aquaculture systems (RAS). Treating diseased fish in RAS is challenging because of the potential to damage nitrifying bacteria in the biofilters. Impaired nitrification can lead to concentrations of ammonia and nitrite that compromise fish welfare. The objective of this study was to determine the effects of a FDA‐approved parasiticide and fungicide, Parasite‐S^® (formalin), on biofilter nitrification. Stable biofilters were exposed once to 0, 9.25, 18.5, 37, or 55.5 mg/L formaldehyde. Total ammonia nitrogen (TAN) and nitrite nitrogen were monitored daily before and throughout the study to quantify biofilter function. Formaldehyde concentrations ≥37 mg/L increased TAN and nitrite nitrogen concentrations, and nitrification did not recover to pre‐exposure concentrations up to 8 day postexposure. On the basis of those results, a second trial was conducted. Stable biofilters were exposed once or on four consecutive days to 9.25 or 18.5 mg/L formaldehyde. Biofilters repeatedly exposed to formaldehyde showed signs of impairment and had variable recovery relative to single exposures. Results of this study may help identify formaldehyde concentrations that can be safely applied to RAS when treating diseased fish.