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This study describes the microbial biomass and community structure depth profiles in biofilters and relates these profiles to the removal of dissolved organic carbon (DOC), biodegradable dissolved organic carbon (BDOC), and specific ozonation byproducts during biofiltration. Samples were taken from the top, middle, and bottom two cm of a 3 cm vertical core extracted from a full-scale rapid sand filter bed at a local drinking water treatment plant. The concentration of natural organic matter (NOM) was measured as DOC after filtering. Microbial community structure profiles were constructed using three methods: BIOLOG sole carbon source utilization patterns, which determines the abilities of intact communities to use various carbon compounds as sole carbon sources; phospholipid fatty acid (PLFA) analysis, which characterizes microbial samples by revealing the relative abundances of signature fatty acids; and DNA amplification fingerprinting (DAF), which provides a qualitative comparison of the genetic similarity between DNA samples extracted from natural samples. The research revealed that removal of the easily assimilated substrates, represented by the quickly degradable fraction of BDOC, within the first few minutes of empty bed contact time (EBCT), lead to a large reduction in biomass from the top to the bottom of the biofilters. Biomass was found to be a function of EBCT, and was independent of filter velocity.