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As a sequencing batch reactor process is operated in the time orientation, it has flexibility of operation, which could easily accomodate aerobic, anoxic, and anaerobic conditions for biological nutrient removal in a reactor through the simple control of aeration. The aeration process of the sequencing batch reactor has been controlled on the basis of dissolved oxygen dynamics. Dissolved oxygen dynamics well represents the characteristics of reactions in a reactor. The first plateau of dissolved oxygen after aeration is related to the balance of oxygen, which is supplied by aeration and utilized by nitrification. The second rapid increase of dissolved oxygen is closely related to the end of nitrification. By applying the control strategy based on dissolved oxygen dynamics, aeration time for the optimal aerobic period is adjusted in a sequencing batch reactor. Aeration time is mainly correlated with the concentration of nitrogen in the influent and could also provide the characteristics of nitrification. The anoxic period could be prolonged through aeration control, so endogenous denitrification is maximized. The removal of phosphorus is enhanced simultaneously.