Abstract: Acoustic tag monitoring technology, an active identification method of acoustic detection technology, can obtain 2D and 3D motion trajectories of fish by receiving and processing the acoustic signals emitting from acoustic tags which are transplanted or tied to fish. It has the advantages of in-situ observation, accurate positioning, simple data processing and good data continuity. The paper introduces the composition and working principle of acoustic tag monitoring technology. A complete data processing method of denoising and cleaning is proposed according to the different characteristics of abnormal data. With this method, the real-time 2D and 3D motion trajectories can be quickly obtained. The distribution of fish motion trajectories and changing rules are analyzed by an example. According to the behavioral response of fish in different water ecological environments, the potential effects and actual toxicity of pollutants or toxic substances in water can be judged directly or indirectly. It provides the references for water quality assessment in aquaculture, monitoring and early warning of water environment, health evaluation of aquatic ecological, as well as evaluation of aquatic ecological restoration.