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One of the biggest challenges in probing the atmospheric boundary layer with small unmanned aerial vehicles is the turbulent 3D wind vector measurement. Several approaches have been developed to estimate the wind vector without using multi-hole flow probes. This study compares commonly used wind speed and direction estimation algorithms that use the direct 3D wind vector measurement using multi-hole probes. This was done using the data of a fully equipped system and by applying several algorithms to the same data set. To cover as many aspects as possible, a wide range of meteorological conditions and common flight patterns were considered in this comparison. The results from the five-hole probe measurements were compared to the pitot tube algorithm, which only requires a pitot-static tube and a standard inertial navigation system measuring aircraft attitude (Euler angles), while the position is measured with global navigation satellite systems. Even less complex is the so-called no-flow-sensor algorithm, which only requires a global navigation satellite system to estimate wind speed and wind direction. These algorithms require temporal averaging. Two averaging periods were applied in order to see the influence and show the limitations of each algorithm. For a window of 4 min, both simplifications work well, especially with the pitot-static tube measurement. When reducing the averaging period to 1 min and thereby increasing the temporal resolution, it becomes evident that only circular flight patterns with full racetracks inside the averaging window are applicable for the no-flow-sensor algorithm and that the additional flow information from the pitot-static tube improves precision significantly.