Flavobacterium psychrophilum, the causative agent of bacterial cold water disease (BCWD), is tolerant of recommended ultraviolet (UV) doses used in recirculation aquaculture systems (RAS). Membrane filtration (MF) is used to remove pathogens from wastewater in many industries, but has not been thoroughly tested in RAS. In this study, bacterial removal efficiencies were assessed between MF and UV treatments over 30 days in an RAS. Bacterial removal efficiencies were not significantly different (p > 0.05) between MF and UV treatments, which removed 98.5 ± 0.4 % and 99.6 ± 0.1 % of total bacteria and 93.2 ± 5.2 % and 92.5 ± 4.1 % of heterotrophic bacteria, respectively. Under laboratory conditions, a MF system was challenged with concentrated doses of F. psychrophilum and achieved 5.8 ± 0.2 log reductions of the pathogen. Therefore, MF represents a potential alternative to UV irradiation and could be used to reduce the prevalence of F. psychrophilum in RAS, potentially reducing the incidence of BCWD and its impact on the aquaculture industry.