From an environmental point of view, hydrogen peroxide (HP) has beneficial attributes compared with other disinfectants in terms of its ready degradation and neutral by-products. The rapid degradation of HP can, however, cause difficulties with regard to safe and efficient water treatment when applied in different systems. In this study, we investigated the degradation kinetics of HP in biofilters from water recirculating aquaculture systems (RAS). The potential effect of HP on the nitrification process in the biofilters was also examined. Biofilter elements from two different pilot-scale RAS were exposed to various HP treatments in batch experiments, and the HP concentration was found to follow an exponential decay. The biofilter ammonia and nitrite oxidation processes showed quick recuperation after exposure to a single dose of HP up to 30 mg L−1. An average HP concentration of 10–13 mg L−1 maintained over 3 h had a moderate inhibitory effect on the biofilter elements from one of the RAS with relatively high organic loading, while the nitrification was severely inhibited in the pilot-scale biofilters from the other RAS with a relatively low organic loading. A pilot-scale RAS, equipped with two biofilter units, both a moving-bed (Biomedia) and a fixed-bed (BIO-BLOK®) biofilter, was subjected to an average HP concentration of ∼12 mg L−1 for 3 h. The ammonium- and nitrite-degrading efficiencies of both the Biomedia and the BIO-BLOK® filters were drastically reduced. The filters had not reverted to pre-HP exposure efficiency after 24 h, suggesting a possible long-term impact on the biofilters.