A common final clarifier is provided downstream of a two-stage activated sludge (AS) system that includes a flow equalization basin (FEB) reactor and a nitritation reactor as the first AS stage and an anammox reactor as the second AS stage. A first return activated sludge (RAS) flow is conducted from the final clarifier to the first AS stage with a low flow rate and a second segregated RAS flow is conducted to the second AS stage with a high flow rate. The FEB reactor is operated as an anoxic reactor to achieve carbonaceous BOD removal; conversion of organic nitrogen to ammonia nitrogen; and, denitrification of recycled nitrite or nitrate nitrogen. The nitritation reactor is operated as an aerobic reactor to achieve oxidation of ammonia nitrogen to nitrite nitrogen by biological nitritation. The anammox reactor is operated at zero or very low dissolved oxygen concentration to achieve nitrogen removal by deammonification.