Water environment monitoring is an important part of environmental monitoring. Due to the constraints of natural condition and time and temporal factors, the traditional monitoring method has some limitations. In recent years, remote Sensing technologies were widely applied in the investigation and monitoring of various pollutions in aquatic environments. Water pollution events like sediment pollution occur frequently in Southwest China. Hence, it is urgent to timely conduct water pollution investigation in target region and takes necessary measures to treat identified water pollution events. Field investigation is reliable but too expensive and time-consuming. Satellite or manned aerial remote sensing have the advantages of region-scale coverage and moderate timeliness, but restricted by the factors of heavy mist, low image resolution, poor human safety, and prohibitive cost. Unmanned Aerial Vehicle (UAV) remote sensing is a very promising approach for water pollution investigation in regional scope, as giving consideration to both accuracy and spatial coverage. In this paper, we demonstrate our practice and experiences in applying UAVs in the investigation of aquatic environment pollution from the aspects of UAV customization and modification, and UAV imagery Interpretation and analysis.