NOVELTY - A biofilter system comprises a main biofilter chamber (110) having an inlet port (104) and an outlet port (106) and containing aerobic and anaerobic bacterial without physical separation; and a pump or an agitator (108) for oxygenating the aerobic and anaerobic bacteria and a timer (112) for timing the oxygenation of the aerobic and anaerobic bacteria.    USE - The system is for removing carbonaceous matter and/or nitrogenous matter from animal waste or aqueous waste resulting from aquaculture by contacting an aqueous source with a mixture of aerobic and anaerobic bacteria in a biofilter chamber, alternating periodically high-oxygen conditions and anoxic conditions, and monitoring an outflow from the biofilter for predetermined levels of carbonaceous matter and/or nitrogenous matter. The animal waste comprising not more than 10% (preferably not more than 1%) solid animal waste is produced by pig, horse, goat, sheep, cow, chicken, turkey, ostrich, emu, llama, or alpaca. The aqueous waste may also be generated by agricultural runoffs, food production or an industrial process, e.g., oil refining process, production of munitions, tanning process, chemical manufacturing process producing fertilizer. (All claimed).    ADVANTAGE - The invention utilizes an alternating-aerobic-anoxic (AAA) process in a single reactor to provide efficient and cheap removal of carbonaceous material and/or nitrogenous material from aqueous waste. An amount of the carbonaceous matter and/or nitrogenous matter in the outflow is reduced by not less than 80% (preferably not less than 90%) from an original amount of the carbonaceous matter and/or nitrogenous matter in the liquid portion of the animal waste.    DETAILED DESCRIPTION - INDEPENDENT CLAIMS are included for the following:    (a) An aquaculture system comprising an aqueous environment, a mechanism for fluidly connecting the aqueous environment with the biofilter system, a mechanism for disinfecting an outflow of the biofilter system, and a mechanism for returning the disinfected outflow to the aqueous environment;    (b) A method of aquaculture wherein fish are grown; and    (c) A system for treating animal waste comprising a first vessel having a first inlet port and a first outlet port and containing a mechanism for degrading animal waste solids and mechanism for separating animal waste solids and animal waste liquid; and a second vessel comprising the biofilter system wherein the inlet port of the biofilter chamber is fluidly connected to the first outlet port of the first vessel.    DESCRIPTION OF DRAWING(S) - The figure shows a biofilter system of the invention.    Main biofilter chamber (110)    Inlet port (104)    Outlet port (106)    Pump or agitator (108)    Timer (112)