Submergence depth of impellers for an oxidation ditch (OD) has significant impact on energy consumption and effluent quality of wastewater treatment plants. The effect of the submergence depth of impellers on the structure of flow fields in an OD was studied using an experimentally validated numerical tool, based on computational fluid dynamics (CFD) model. The two-phase gas–liquid model and the 3D RNG k–ε turbulence model were used to describe flow in ODs. The pressure implicit with splitting of operators algorithm was used to solve velocity and pressure. The volume of fluid (VOF) method was used to simulate free-water surface. The concept of submergence depth ratio representing the impeller’s submergence depth h to the total water depth H, h/H, was introduced to analyze the simulation results. Under different submergence depth ratios of impellers in an OD, the velocity fields were computed and analyzed, which shows that with the submergence depth ratio 0.45, the percentage of VOF particles with velocity greater than 0.3 m/s to the volume of entire fluid particles is the greatest, and that the velocity distribution is more uniform along water depth, being much useful for preventing sludge from settling in ODs. Therefore, the submergence depth ratio 0.45 is called the optimal submergence ratio, and its corresponding operating condition will better improve the efficiency of an OD wastewater treatment system.