Seawater filters containing expanded clay (EC) and granulated activated carbon (GAC) media were operated for 14 months. The biological activity found after concentrating the backwashed sludge was analysed by fluorescence in situ hybridisation (FISH), scanning electron microscopy (SEM) and 16 s rRNA gene cloning. FISH and SEM analyses confirmed the presence of extracellular polymeric substances derived from bacteria, and planktonic and benthic eukaryotic microorganisms were found. The bacterial community distribution examined by cloning and sequencing of the 16 s rRNA bacterial genes demonstrated that both filter populations were dominated by the Proteobacteria class, accounting for 68 and 50% of the EC and GAC filter populations, respectively, followed by Bacteroidetes (10 and 22%), Planctomycetes (6 and 10%), Verrucomicrobia (6 and 13%) and others that occurred at lesser extents (<9%). No noticeable differences were observed between the two filters, although the delta-proteobacteria phylum only appeared in the EC filter. Dominant classes observed in both EC and GAC libraries are close to seawater reverse osmosis membrane libraries, and most of them are often linked to biofilm promoters, suggesting that both types of media could act as accumulators of biofilm promoters. (C) 2013 Elsevier B.V. All rights reserved.