Mapping and prediction of inundated areas is increasingly important for climate change adaptation and emergency preparedness. Flood forecasting tools and flood risk models have to be compared to observed flooding patterns for training, calibration, validation and benchmarking. At regional to continental scale, satellite earth observation is the established method for surface water extent (SWE) mapping and several operational global-scale data products are available. However, the spatial resolution of satellite-derived SWE maps remains a limiting factor, especially in low-lying areas with complex hydrography, such as Denmark. We collected thermal imagery using an unmanned airborne system (UAS) for three areas in Denmark shortly after major flooding events. We combined the thermal imagery with an airborne lidar-derived high-resolution digital surface model of the country to retrieve high-resolution (40 cm) SWE maps. The resulting SWE maps were compared to low-resolution SWE maps derived from satellite earth observation (EO). We conclude that UAS have significant potential for SWE mapping at intermediate scales, can bridge the scale gap between ground observations and satellite EO and can be used to benchmark and validate SWE mapping products derived from satellite EO as well as models predicting inundation.