This study presents the results from a combined aerial survey performed with a hexacopter and a gyrocopter over a part of the Elbe estuary near Hamburg, Germany. The survey was conducted by the Federal Institute of Hydrology, Germany, and the Fraunhofer Application Center for Multimodal and Airborne Sensors as well as by a contracted engineering company with the aim to acquire spatial thermal infrared (TIR) data of the Hahnöfer Nebenelbe, a branch of the Elbe estuary. Additionally, RGB and NIR data was captured to facilitate the identification of water surfaces and intertidal mudflats. The temperature distribution of the Elbe estuary affects all biological processes and in consequence the oxygen content, which is a key parameter in water quality. The oxygen levels vary in space between the main fairway and side channels. So far, only point measurements are available for monitoring and calibration/validation of water quality models. To better represent this highly dynamic system with a high spatial and temporal variability, tidal streams, heating and cooling, diffusion and mixing processes, spatially distributed data from several points of time within the tidal cycle are necessary. The data acquisition took place during two tidal cycles over two subsequent days in the summer of 2015. While the piloted gyrocopter covered the whole Hahnöfer Nebenelbe seven times, the unmanned hexacopter covered a smaller section of the branch and tidal mudflats with a higher spatial and temporal resolution (16 coverages of the subarea). The gyrocopter data was acquired with a thermal imaging system and processed and georeferenced using the structure from motion algorithm with GPS information from the gyrocopter and optional ground control points. The hexacopter data was referenced based on ground control points and the GPS and position information of the acquisition system. Both datasets from the gyrocopter and the hexacopter are corrected for the effects of the atmosphere and emissivity of the water surface and compared to in situ measurements, taken during the data acquisition. Of particular interest is the effect of the observation angle on the brightness temperature acquired by the wide angle lenses on the platforms, which is up to 40° at the margins of the imagery. Here, both datasets show deviating temperatures, which are probably not due to actual temperature differences. We will discuss the position accuracy achieved over the water areas, the adaptation of atmospheric and emissivity correction to the observation angle and subsequent improvement of the temperature data. With two datasets of the same research area at different resolutions we will investigate the effects of the acquisition platforms, acquisition system and resolutions on the accuracy of the remotely sensed temperatures as well as their ability to represent temperature patterns of tidal currents and mixing processes.