The paper presents an efficient methodology of water body extent estimation based on remotely sensed data collected with UAV (Unmanned Aerial Vehicle). The methodology includes the data collection with selected sensors and processing of remotely sensed data to obtain accurate geospatial products that are finally used to estimate water body extent. Three sensors were investigated: RGB (Red Green Blue) camera, thermal infrared camera, and laser scanner. The platform used to carry each of these sensors was an Aibot X6—a multirotor type of UAV. Test data was collected at 6 sites containing different types of water bodies, including 4 river sections, an old river bed, and a part of a lake shore. The processing of collected data resulted in 2.5-D and 2-D geospatial products that were used subsequently for water body extent estimation. Depending on the type of used sensor, the created geospatial product, and the type of the water body and the land cover, three strategies employing image processing tools were developed to estimate water body range. The obtained results were assessed in terms of classification accuracy (distinguishing the water body from the land) and geometrical planar accuracy of the water body extent. The product identified as the most suitable in water body detection was four bands RGB+TIR (Thermal InfraRed) ortho mosaic. It allowed to achieve the average kappa coefficient of the water body identification above 0.9. The planar accuracy of water body extent varied depending on the type of the sensor, the geospatial product, and the test site conditions, but it was comparable with results obtained in similar studies.