Recalcitrant chemical oxygen demand (COD) of a liquid is reduced in a water treatment system. The method includes pretreating the liquid in a pretreatment unit to remove indigenous bacteria or microbes to a population level below which the indigenous organisms can interfere with the screened and externally introduced microorganisms. The liquid is then provided to a reactor that has a filter bed formed with a carrier material. Special microbes are screened and used to colonize the carrier material to remove recalcitrant COD. A biofilm is cultured on the surface of the carrier material to immobilize the screened microbes in the reactor. The method further includes percolating the liquid from the pretreatment unit through the filter bed colonized with the screened microbes to degrade at least part of the recalcitrant COD under aerobic conditions. In one embodiment, the filter is formed with biological granular activated carbon (GAC) as the carrier material and the screened microbes comprise at least one microbial species selected from the group consisting of Bacillus, Comamonas, Arthrobacter, Micrococcus, Pseudomonas, Pediococcus, Achromobacter, Flavobacterium, Mycobacterium, Rhodanobacter, Stenotrophomonas and Yeast.