Stream velocity and flow are very important parameters that must be measured accurately to develop effective water resource management plans. There are various methods and tools to measure the velocity but, nowadays, image-based methods are a promising alternative that does not require physical contact with the water body. The current study describes the application of a low cost unmanned aerial vehicle that was selected in order to capture a video over a specific reach of Aggitis River in Greece. The captured frames were analyzed by three different software (PIVlab, PTVlab, and KU-STIV) in order to estimate accurately the surface water velocity. These three software also represent three different image-based methodologies. Although there are differences among these three methods, the analysis produced similar trends for all. The velocity ranged between 0.02 and 3.98 m/s for PIVlab, 0.12 and 3.44 m/s for PTVlab, and 0.04 and 3.99 m/s for KU-STIV software. There were parts, especially in the existing vegetation, where differences were observed. Further applications will be examined in the same or different reaches, to study the parameters affecting the analysis. Finally, the image-based methods will be coupled with verification measurements by a current meter to produce more rigorous results.