Growth, biofilm formation, antagonism and residence time in green seawater tanks maintained under fish rearing conditions of Phaeobacter 27-4 were studied in commercial biofilters made from plastic, sintered glass and ceramic. Phaeobacter reached 108–109 CFU cm−3 and formed rosettes in all materials, but a multilayer biofilm was only observed in the ceramic biofilters. In sterile seawater, plastic and ceramic biofilters reduced Vibrio anguillarum and V. splendidus concentration in one-two Log after 24–48 h, showing 102–103 CFU mL−1. Sintered glass biofilters only inactivated V. anguillarum. In Marine Broth, sintered glass and ceramic biofilters inhibited V. anguillarum growth in two-three Log, showing 104–105 CFU mL−1 after 24 h. Plastic biofilters reduced V. anguillarum concentration in one Log after 48 h. V. splendidus growth was only inhibited by sintered glass and ceramic biofilters in one-two Log, showing 107 CFU mL−1 after 24 h. Phaeobacter also diminished biofilters colonization by the pathogens, both in seawater and in MB. Phaeobacter residence time in green seawater tanks maintained under fish rearing conditions was longer with sintered glass and ceramic biofilters. The latest showed the lowest detachment and, after 11 days, Phaeobacter (106 bacteria·cm−3) covered more than 80% of biofilters total culturable bacteria. DGGE profiles showed that Phaeobacter biofilters stabilizes the green seawater bacterial microbiota.