Peracetic acid (PAA) is a powerful disinfectant with a wide spectrum of antimicrobial activity. PAA and hydrogen peroxide (HP) degrade easily to oxygen and water and have potential to replace formalin in aquaculture applications to control fish pathogens, for example the ectoparasite, Ichthyophthirius multifiliis.We studied water phase PAA and HP decay in three aquaculture situations, i) batch experiments with two types of system waters, ii) PAA decay at different fish densities, and iii) degradation of PAA in submerged biofilters of recirculating aquaculture systems (RAS). Furthermore, effect of PAA on the nitrification activity and the composition of the nitrifying population were investigated.PAA and HP decay showed first order kinetics. High dosage PAA/HP in water with low COD inhibited HP removal, which was not observed in water having a higher COD content. PAA decay was significantly related to fish stocking density, with half life constants for PAA of 4.6 and 1.7 h at 12 and 63 kg m− 3, respectively.PAA application to RAS biofilter showed rapid exponentially decay with half life constants of less than 1 h, three to five times faster than the water phase decay rates.Biofilter surface specific PAA removal rates ranged from 4.6 to 13.9 mg PAA m− 2 h− 1 and was positively correlated to the nominal dosage. Low PAA additions (1.0 mg L− 1) caused only minor impaired nitrification, in contrast to PAA application of 2.0 and 3.0 mg L− 1, where nitrite levels were significantly increased over a prolonged period, albeit without fish mortality. The dominant ammonium oxidizer was Nitrosomonas oligotropha and the dominant nitrite oxidizer was Nitrospira. Based on the present findings and other recent results from field and in vitro studies, application perspectives of PAA are discussed.