Flow measurement in shallow water is of great significance for hydrological observation in intracontinental aera, which can promote the development of flood control irrigation and other water conservancy projects. The broadband acoustic Doppler current profiler (ADCP) can accurately monitor the information of the flow velocity in the water area. The broadband ADCP used for shallow water flow measurement is not easy to achieve better velocity accuracy in the narrow flow layer and is vulnerable to local turbulence interference in the narrow flow layer. To solve the above problems, this paper proposes a retrieval method of the optimal value of the solution results based on η criterion, optimizes the local correlation evaluation method, and completes the development of the ADCP system based on system on chip (SoC). The effect of the algorithm is further verified by the radial velocity generated by the beam-velocity angle. The outdoor sailing experiment is carried out. When the radial layer thickness is 6. 3 cm with turbulence interference, the velocity precision and degree of accuracy can be improved by 37% and 77% respectively after the algorithm is applied, 66% and 72% respectively in the case of low SNR. The error between the angle calculated according to the speed measurement value and the set value is 3. 06°, which is reduced to 2. 60°after algorithm processing. The angle error obtained by the error relation of measured speed can reach 0. 6°. In the boat experiment in a calm lake, the standard deviation of the system can reach 1 mm/ s, and the error of interlayer velocity can reach 1 mm/ s, which is close to the theoretical velocity distribution.