A biologically active reactor system for the treatment of wastewater comprises one or more submerged denitrification reactors having coarse media particles and a fixed biological film comprising biologically anoxic active microorganisms. One or more submerged aerated filters are in fluid communication with the one or more submerged denitrification reactor, the submerged aerated filter comprising coarse media particles and a fixed biological film comprising biologically aerobic microorganisms for oxidation of organic matter. One or more deep bed denitrification filters for removal of suspended solids and denitrification of oxidized nitrogens are in fluid communication with the one or more submerged aerated filters, the deep bed denitrification filter comprising fine media particles of less than 6 mm. Effluent from the submerged aerated filter is recycled to the submerged denitrification reactor for pre-denitrification prior to being piped to the deep bed denitrification filter. During the method, wastewater influent along with treated effluent from the submerged aerated filter is fed to a submerged denitrification reactor.