Methods and systems for utilizing biological wastewater treatment processes to remove nutrients from wastewater containing reduced sulfide compounds may include treating the wastewater in an anaerobic zone, an anoxic zone, and an aerobic zone. The wastewater is first treated in the anaerobic zone to uptake residual biodegradable organic material using specialized bacteria known as phosphorus accumulating organisms (“PAOs”) and glycogen accumulating organisms (“GAOs”). After treatment in the anaerobic zone, the wastewater is treated in an anoxic zone to convert nitrates to nitrogen gas and sulfur to sulfates. Following treatment in the anoxic zone, the wastewater is treated in the aerobic zone to oxidize ammonia to nitrate and to complete removal of phosphorus. After treatment in the aerobic zone, the wastewater may be treated in other zones, or may be delivered to a liquid-solids treatment stage.