Dissolved organic matter (DOM) plays a pivotal role in drinking water treatment, influencing the performance of unit processes and final water quality (e.g. disinfection byproduct risk). Biofiltration is an effective method of reducing DOM, but currently lacks a comprehensive appreciation of the association between microbial profiles and biofiltration performance. In this study, bench-scale biofiltration units inoculated with microbial consortia from river and soil matrices were operated successively for comparing their efficacy in terms of DOM removal. The results showed that biofiltration units receiving soil microbes were significantly superior (p < 0.05) to those receiving river inoculated microbes in terms of decomposing DOM recalcitrant fractions and reducing DBP formation potential, resulting in DOC and DBP precursor removals of up to 58.4 % and 87.9 %, respectively. Characterization of the taxonomic composition revealed that differences in the microbial assembly of the two biofilter groups were subject to deterministic rather than stochastic factors. Furthermore, more complicated interspecific relationships and niche structures in soil inoculated biofilters were deciphered by co-occurrence network, providing a plausible profile on a taxonomic division of labor in DOM stepwise degradation. Accordingly, the contribution of microbial compositions was found to be of greater importance than the GAC mass and biomass attached to the media. Thus, this study has advanced the understanding of microbial-mediated DOM decomposition in biofiltration, and also provided a promising strategy for enhancing the process for water use via developing appropriate engineered consortia of bacteria.