Peracetic acid (PAA; CH3CO3H) has shown promise as an efficacious, environmentally-friendly disinfectant in aquaculture; however, PAA is not currently approved in the United States for treating systems when food fish are present and is only permitted for use in aquaculture as a surface disinfectant. There is significant interest in the aquaculture industry for using PAA as a water disinfectant to reduce or eliminate potential opportunistic pathogens (e.g., Flavobacterium spp). The efficacy of PAA in killing a range of bacteria, fungi, yeasts, and viruses has been demonstrated, and its rapid degradation into non-toxic byproducts of acetic acid, hydrogen peroxide, and water largely eliminates pollution and discharge issues. Previous research on PAA application in aquaculture settings has primarily focused on disease prevention through PAA’s bactericidal activity. Additionally, several toxicity studies indicate that low-dose PAA treatments are tolerated by commercially raised rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) at various life stages. Intensive fish production technologies, such as recirculating aquaculture systems (RAS) commonly used to raise these species, rely on microbial-based treatment processes, including nitrifying biofilters. Bacteria established on biofilter media are integral to converting toxic fish metabolites (i.e., ammonia) into less harmful nitrate. Because PAA is a broad-spectrum antimicrobial product, nitrification could be impaired if biofilters are exposed to sufficient concentrations of PAA, due to the destruction of nitrifying bacteria. Disruption of nitrification, even if temporary, can result in significant adverse outcomes for fish, as ammonia and nitrite can be highly toxic when above certain concentrations. As such, baseline research is essential to identify biofiltration-safe protocols for administering PAA in RAS. Several studies investigating low-dose PAA application in RAS have been carried out at The Conservation Fund Freshwater Institute (Shepherdstown, WV, USA) in recent years, and this presentation will describe these investigations in depth and will summarize our research findings.