Bacteria indigenous to water distribution systems were used to grow multispecies biofilms within continuous-flow slide chambers. Six flow chambers were also inoculated with an Escherichia coli isolate obtained from potable water. The effect of disinfectants on bacterial populations was determined after exposure of established biofilms to 1 ppm of hypochlorous acid (ClOH) for 67 min or 4 ppm of monochloramine (NH 2 Cl) for 155 min. To test the ability of bacterial populations to initiate biofilm formation in the presence of disinfectants, we assessed the biofilms after 2 weeks of exposure to residual concentrations of 0.2 ppm of ClOH or 4 ppm of NH 2 Cl. Lastly, to determine the effect of recommended residual concentrations on newly established biofilms, we treated systems with 0.2 ppm of ClOH after 5 days of growth in the absence of disinfectant. Whole-cell in situ hybridizations using fluorescently tagged, 16S rRNA-targeted oligonucleotide probes performed on cryosectioned biofilms permitted the direct observation of metabolically active bacterial populations, including certain phylogenetic groups and species. The results of these studies confirmed the resistance of established bacterial biofilms to treatment with recommended levels of disinfectants. Specifically, Legionella pneumophila, E. coli, and  and ␦ proteobacteria were identified within biofilms both before and after treatment. Furthermore, although it was undetected using routine monitoring techniques, the observation of rRNA-containing E. coli within biofilms demonstrated not only survival but also metabolic activity of this organism within the model distribution systems. The persistence of diverse bacterial species within disinfectant-treated biofilms suggests that current testing practices underestimate the risk to immunocompromised individuals of contracting waterborne disease.Assessment of the microbiological safety of drinking water is based largely on the routine monitoring of water supplies for the presence of total coliforms and Escherichia coli. Detection of E. coli is considered indicative of recent fecal contamination and of the potential presence of enteric pathogens, while the presence of total coliforms is indicative of poor water quality.Whereas routine water quality measurements assess the presence of planktonic bacteria, the vast majority of bacteria indigenous to aquatic environments exist attached to solid particles or surfaces. Within water distribution systems, significant bacterial populations exist as complex, structurally heterogeneous biofilms attached to pipe surfaces. Residence within these complex matrices provides organisms with higher localized nutrient concentrations than are commonly found in drinking waters (10,14,18,22), and recent studies have shown that attached bacteria are more metabolically active than are their free-living counterparts (26, 29). Furthermore, biofilms afford bacteria significant protection from disinfecting agents (3, 31, 35), including hypochlorous acid and monochloramine. Biofilms are dynamic ...