A mainstream deammonification process for removing ammonium from a wastewater stream, comprising: clarifying the wastewater stream in a primary clarifier and producing a carbon rich primary effluent; directing a first portion of the carbon rich primary effluent to a biological treatment reactor and removing carbon from the carbon rich primary effluent to produce treated wastewater; after treating the first portion of the carbon rich primary effluent in the biological treatment reactor, directing the treated wastewater into an integrated fixed film activated sludge (IFAS) deammonification reactor that is provided with intermittent aeration including periods of air on and periods of air off; directing a second portion of the carbon rich primary effluent to the IFAS deammonification reactor and in the process bypassing the biological treatment reactor; injecting the second portion of the carbon rich primary effluent into the IFAS deammonification reactor during periods of air off and refraining from injecting the second portion of the carbon rich primary effluent into the IFAS deammonification reactor during periods of air on, wherein the second portion of the carbon rich primary effluent is mixed with the treated wastewater in the IFAS deammonification reactor to form a wastewater mixture; maintaining anoxic conditions in the IFAS reactor during periods of air off; in the IFAS deammonification reactor, removing ammonium from the wastewater mixture by a nitritation and anammox process and wherein the supply of readily biodegradable carbon to the IFAS reactor during periods of air off gives rise to partial denitrification by converting some nitrate to nitrite; and after removing ammonium from the wastewater mixture, directing the wastewater mixture to a secondary clarifier and producing a secondary effluent and a clarifier underflow, and recycling at least a portion of the underflow to the IFAS deammonification reactor. clarifying the wastewater stream in a primary clarifier and producing a carbon rich primary effluent; directing a first portion of the carbon rich primary effluent to a biological treatment reactor and removing carbon from the carbon rich primary effluent to produce treated wastewater; after treating the first portion of the carbon rich primary effluent in the biological treatment reactor, directing the treated wastewater into an integrated fixed film activated sludge (IFAS) deammonification reactor that is provided with intermittent aeration including periods of air on and periods of air off; directing a second portion of the carbon rich primary effluent to the IFAS deammonification reactor and in the process bypassing the biological treatment reactor; injecting the second portion of the carbon rich primary effluent into the IFAS deammonification reactor during periods of air off and refraining from injecting the second portion of the carbon rich primary effluent into the IFAS deammonification reactor during periods of air on, wherein the second portion of the carbon rich primary effluent is mixed with the treated wastewater in the IFAS deammonification reactor to form a wastewater mixture; maintaining anoxic conditions in the IFAS reactor during periods of air off; in the IFAS deammonification reactor, removing ammonium from the wastewater mixture by a nitritation and anammox process and wherein the supply of readily biodegradable carbon to the IFAS reactor during periods of air off gives rise to partial denitrification by converting some nitrate to nitrite; and after removing ammonium from the wastewater mixture, directing the wastewater mixture to a secondary clarifier and producing a secondary effluent and a clarifier underflow, and recycling at least a portion of the underflow to the IFAS deammonification reactor.