This study assesses the suitability to use RGB and thermal infrared imagery acquired from an UAV to measure surface flow velocities of rivers. The reach of a medium-scale river in Hungary is investigated. Image sequences with a frame rate of 2 Hz were captured with two sensors, a RGB and an uncooled thermal camera, at a flying height that ensures the visibility of both shores. The interior geometry of both cameras were calibrated with an in-house designed target field. The image sequences were automatically co-registered to account for UAV movements during the image acquisition. The TIR data was processed to keep loss-free image information solely in the water area and to enhance the signal to noise ratio. Image velocimetry with PIV applied to the TIR data and PTV applied to the RGB data was utilised to retrieve surface flow velocities. Comparison between RGB and TIR data reveal an average deviation of about 0.01 m/s. Future studies are needed to evaluate the transferability to other non-regulated river reaches.