Traditional bird monitoring methods have the limitations of long investigation time, large consumption of manpower and material resources, as well as inaccurate identifications. In recent years, unmanned aerial vehicle (UAV) remote sensing technology has been widely used in the field of ecology, however, it is still a lack of developed methods for its application in bird survey. In this study, a micro-UAV (DJI Mavic 2) equipped with a visible light camera was used to conduct a waterfowl survey in the West Dongting Lake National Nature Reserve in Hunan Province. Four survey areas were selected inside the reserve where the target species were concentrated. With flight routes in each area planned and the flight and shooting parameters set appropriately, remote sensing data were collected (Fig. 1). Meanwhile, the birds’ response to the disturbance caused by the shooting process was ranked and recorded (Table 1). Subsequently, the image splicing software PTGui Pro 11.0 was employed to splice the collected images and adjusted their color balance. Finally, based on the synthesized remote sensing image, the classification and annotation table of waterfowl was established and the waterfowl in the image were manually interpreted. Also, the disturbance ranks of the investigation to the waterfowl was analyzed statistically. We conducted 11 flights in this study, of which the largest flight sites had an area of 18 hm2 and the resolution of 0.012 m/pixel at the flight altitude of 75 m. We successfully obtained data from ten survey flights. We tried to identify and count, in our obtained images, six main waterfowl species with relatively large body size: Ardea alba, A. cinerea, Anas crecca, Mareca falcata, Cygnus columbianus and Vanellus vanellus (Table 2, Fig. 2). The results showed that the four target species can be identified and counted accurately with the remote sensing images, however, the A. crecca and M. falcata could not be distinguished from each other. Alarm rating records show that the drone investigation had a minor impact on waterfowl. In conclusion, it is feasible to conduct rapid remote sensing monitoring of large and medium sized waterfowl in wetland based on micro-UAV equipped with visible light cameras. In order to achieve relatively higher accuracy of interpretation and prevent excessive interference to waterfowl at the same time, parameters such as flight altitude, flight speed and image overlap need to be set appropriately.