In aquaculture, water quality is influenced by excessive feeding, a high breeding density, the species composition and the distribution of algae species. Traditional buoys can only collect water quality data at a fixed depth, and it is impossible to measure the water quality at different depths in the water column. Sea waves are common in the open ocean and influence data acquisition systems via wave forces, which affect the accuracy of data collection. Considering the above problems, a data acquisition control system with automatic lifting is designed. The underwater acquisition system collects water quality data and sends the data to a microcontroller. The microcontroller sends a displacement control signal to a PLC according to the processed data. The PLC automatically develops the corresponding acceleration and deceleration operating curves according to the displacement. A fuzzy PID self-tuning control method is used to accurately control the speed and steering of the stepping motor, and an IIR digital filter is designed to reduce the interference from sea waves. The simulation results show that the stepping motor responds quickly, the speed of the stepping motor is stable, and the data acquisition time is reduced based on the proposed algorithm. Moreover, wave interference is largely mitigated, and the system is generally stable.