The United States Marine Shrimp Farming Program (USMSFP) introduced a new technology for shrimp farming called recirculating raceway system. This is a zero-water exchange system capable of producing high-density shrimp yields. However, this system produces wastewater characterized by high levels of ammonia, nitrite, and nitrate due to 40% protein diet for the shrimp at a high density of 1,000 shrimp per square meter. The high concentrations of nitrate and nitrite (greater than 25 ppm) are toxic to shrimp and cause high mortality. So treatment of this wastewater is imperative in order to make shrimp farming viable. One simple method of treating high-nitrogen wastewater is the use of a sequencing batch reactor (SBR). An SBR is a variation of the activated sludge process, which accomplishes many treatment events in a single reactor. Removal of ammonia and nitrate involved nitrification and denitrification reactions by operating the SBR aerobically and anaerobically in sequence. Initial SBR operation successfully removed ammonia, but nitrate concentrations were too high because of carbon limitation in the shrimp production wastewater. An optimization study revealed the optimum carbon to nitrogen (C:N) ratio of 10:1 for successful removal of all nitrogen species from the wastewater. The SBR operated with a C:N ratio of 10:1 with the addition of molasses as carbon source successfully removed 99% of ammonia, nitrate, and nitrite from the shrimp aquaculture wastewater within 9 days of operation.