To improve the water quality in the shrimp aquaculture, a sequencing batch reactor (SBR) has been tested for the treatment of shrimp wastewater. A SBR is a variation of the activated sludge biological treatment process. This process uses multiple steps in the same tank to take the place of multiple tanks in a conventional treatment system. The SBR accomplishes equalization, aeration, and clarification in a timed sequence in a single reactor basin. This is achieved in a simple tank, through sequencing stages, which include fill, react, settle, decant, and idle. A laboratory scale SBR and a pilot scale SBR was successfully operated using shrimp aquaculture wastewater. The wastewater contained high concentration of carbon and nitrogen. By operating the reactor sequentially, viz, aerobic and anoxic modes, nitrification and denitrification were achieved as well as removal of carbon in a laboratory scale SBR. To be specific, the initial chemical oxygen demand (COD) concentration of 1,593 mg/l was reduced to 44 mg/l within 10 days of reactor operation. Ammonia in the sludge was nitrified within 3 days. The denitrification of nitrate was achieved by the anaerobic process and 99% removal of nitrate was observed. Based on the laboratory study, a pilot scale SBR was designed and operated to remove excess nitrogen in the shrimp wastewater. The results mimicked the laboratory scale SBR.