In this study, biofilters (BFs) packed with inorganic (ceramsite and lava rock) and organic (fibrous carrier and biological ball) materials were applied in a tide-flow mode at three flooded/drained (F/D) time ratios (16/8 h, 12/12 h and 8/16 h) to treat heavily polluted river water. The results showed that higher ammonium and phosphorus removals were achieved with BFs filled with ceramsite (95-97% and 76-77%) and lava rock (87-92% and 84-94%), while fibrous carrier-packed BFs obtained better total nitrogen removal (37-44%). Moreover, the F/D time ratio of 16/8 h was slightly preferable for pollutant removal. High-throughput sequencing analysis illustrated that the relative abundance of potential denitrifiers that developed on organic media was much higher than those on inorganic substrates. The results indicated that the combination of inorganic materials and fibrous carriers as substrates could be an effective strategy for enhancing overall pollutant removal in BFs.