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A pilot study employing two parallel trains of two-stage biofiltration, i.e., a sand/anthracite (SA) biofilter followed by a biologically-active granular activated carbon (GAC) contactor, was conducted to test the efficiency, feasibility and stability of biofiltration for removing natural organic matter (NOM) after coagulation in a drinking water treatment plant. Results showed the biofiltration process could effectively remove turbidity ( 24% of dissolved organic carbon (DOC), >57% of UV254, and >44% of SUVA254), where the SA biofilters showed a strong capacity for turbidity removal, while the GAC contactors played the dominant role in NOM removal. The vertical profile of water quality in the GAC contactors indicated the middle-upper portion was the critical zone for the removal of NOM, where relatively higher adsorption and enhanced biological removal were afforded. Fluorescence excitation-emission matrix (EEM) analysis of NOM showed that the GAC contactors effectively decreased the content of humic-like component, while protein-like component was refractory for the biofiltration process. Nutrients (NH4-N and PO4-P) supplementation applied upstream of one of the two-stage biofiltration trains (called engineered biofiltration) stimulated the growth of microorganisms, and showed a modest effect on promoting the biological removal of small non-aromatic compositions in NOM. Redundancy analysis (RDA) indicated influent UV254 was the most explanatory water quality parameter for GAC contactors’ treatment performance, and a high load of UV254 would result in significantly reduced removals of UV254 and SUVA254.