Most Autonomous Underwater Vehicles (AUVs) mount an Acoustic Doppler Current Profilers (ADCP). Data from this sensor are rarely used in scientific studies due to the complexity of its processing and the lack of validation. Aside of that, AUV operators lack a set of guidelines regarding the optimal navigation modes and AUV-borne ADCP configurations to obtain the most accurate data possible. This study compares 12.6 hours of AUV-borne ADCP currents measurements, taken in different AUV navigation modes and ADCP configurations, to those of a moored AWAC. Results show RMS errors of 5 cm/s for U (East) and V (North) measures and of 2 cm/s for vertical currents measures for most of the navigation modes. Cell size is found to be the most influential parameter in data accuracy and yo-yo type of surveys are proved to be as accurate as constant depth ones.