A previously isolated indigenous strain of Pseudomonas sp. was used to treat effluents, a synthetic and an industrial-containing benzalkonium chloride (BAC), in continuous upflow biofilm aerobic reactors. The reactor used to treat the synthetic effluent was constructed from Plexiglas® and filled with hollow polyvinyl chloride (PVC) cylinders as support material, whereas the one used to treat the industrial effluent was constructed from PVC and had a high recirculation flow rate and lightweight expanded clay aggregate (LECA®) as support material. Biodegradation was evaluated by spectrophotometry, HPLC, and microbial growth. Detoxification was evaluated by using Vibrio fisheri , Pseudokirchneriella subcapitata , and Lactuca sativa as test organisms. Maximal BAC influent concentrations were of 383.4 and 1172.0 mg L −1 respectively, which corresponds to a maximal organic load of 49.8 and 146.5 g BAC m −3  day −1 . The efficiency of the reactors was higher than 99.3% in terms of compound removal and 97.0% in terms of COD removal. Complete detoxification of the effluent was demonstrated for the synthetic effluent, whereas a toxicity removal higher than 97% was reached in the case of the industrial effluent. The promising behavior of the isolated indigenous strain to degrade BAC in continuous reactors allows us to suggest its possible use in remediation processes.