A method of treating a waste stream having anaerobically biodegradable components, comprising: a. providing a system comprising an anaerobic membrane bioreactor comprising an anaerobic reactor and a membrane separation unit; b. feeding a waste stream having the anaerobically biodegradable components into an anaerobic reactor and forming mixed liquor; c. reacting the biodegradable components with anaerobic biomass in the anaerobic reactor to reduce the amount of biodegradable components and in the process produce biomass and biogas; d. stratifying the mixed liquor in the anaerobic reactor into three mixed liquor zones by forming a first lower mixed liquor zone where the mixed liquor in the first lower mixed liquor zone includes a concentration of solids, including biological flocs and inorganic precipitated solids that form and tend to settle to the bottom of the anaerobic reactor, forming a second mixed liquor zone above the first lower mixed liquor zone where the mixed liquor in the second mixed liquor zone includes a solids concentration less than the concentration of solids in the first lower mixed liquor zone, and forming a third mixed liquor zone in the upper portion of the reactor and over the second mixed liquor zone where the third mixed liquor zone includes solids that tend to float to the upper portion of the anaerobic reactor and wherein the solids concentration in the third mixed liquor zone is higher than the solids concentration in the second mixed liquor zone; e. providing at least one mixer in the first mixed liquor zone and generating a mixing action in the first lower mixed liquor zone for mixing the mixed liquor and solids therein; f. providing at least one mixer in the third mixed liquor zone and generating a mechanical mixing action in the third mixed liquor zone and mixing the mixed liquor and solids therein to maintain the solids in the third mixed liquor zone in suspension and to prevent the solids from forming a blanket in the third mixed liquor zone and for enhancing reactions between anaerobically biodegradable components and the biomass; g. directing mixed liquor from the second mixed liquor zone in the anaerobic reactor to a membrane separation unit and separating the mixed liquor into a permeate stream and a retentate stream; h. recycling at least a portion of the retentate stream to the anaerobic reactor and mixing the retentate stream with the mixed liquor in the reactor; and i. wherein the mixed liquor in the second mixed liquor zone is generally unmixed such that the mixing action in the first and third mixed liquor zones is greater than the mixing action in the second mixed liquor zone. a. providing a system comprising an anaerobic membrane bioreactor comprising an anaerobic reactor and a membrane separation unit; b. feeding a waste stream having the anaerobically biodegradable components into an anaerobic reactor and forming mixed liquor; c. reacting the biodegradable components with anaerobic biomass in the anaerobic reactor to reduce the amount of biodegradable components and in the process produce biomass and biogas; d. stratifying the mixed liquor in the anaerobic reactor into three mixed liquor zones by forming a first lower mixed liquor zone where the mixed liquor in the first lower mixed liquor zone includes a concentration of solids, including biological flocs and inorganic precipitated solids that form and tend to settle to the bottom of the anaerobic reactor, forming a second mixed liquor zone above the first lower mixed liquor zone where the mixed liquor in the second mixed liquor zone includes a solids concentration less than the concentration of solids in the first lower mixed liquor zone, and forming a third mixed liquor zone in the upper portion of the reactor and over the second mixed liquor zone where the third mixed liquor zone includes solids that tend to float to the upper portion of the anaerobic reactor and wherein the solids concentration in the third mixed liquor zone is higher than the solids concentration in the second mixed liquor zone; e. providing at least one mixer in the first mixed liquor zone and generating a mixing action in the first lower mixed liquor zone for mixing the mixed liquor and solids therein; f. providing at least one mixer in the third mixed liquor zone and generating a mechanical mixing action in the third mixed liquor zone and mixing the mixed liquor and solids therein to maintain the solids in the third mixed liquor zone in suspension and to prevent the solids from forming a blanket in the third mixed liquor zone and for enhancing reactions between anaerobically biodegradable components and the biomass; g. directing mixed liquor from the second mixed liquor zone in the anaerobic reactor to a membrane separation unit and separating the mixed liquor into a permeate stream and a retentate stream; h. recycling at least a portion of the retentate stream to the anaerobic reactor and mixing the retentate stream with the mixed liquor in the reactor; and i. wherein the mixed liquor in the second mixed liquor zone is generally unmixed such that the mixing action in the first and third mixed liquor zones is greater than the mixing action in the second mixed liquor zone.