Precise underwater geodetic positioning remains a challenge. Measurements combining surface positioning (GNSS) with underwater acoustic positioning are generally performed from research vessels. Here we tested an alternative approach using a small Unmanned Surface Vehicle (USV) with a compact GNSS/Acoustic experimental set-up, easier to deploy, and more cost-effective. The positioning system included a GNSS receiver directly mounted above an Ultra Short Baseline (USBL) module integrated with an inertial system (INS) to correct for the USV motions. Different acquisition protocols, including box-in circles around transponders and two static positions of the USV, were tested. The experiment conducted in the shallow waters (40 m) of the Bay of Brest, France, provided a data set to derive the coordinates of individual transponders from two-way-travel times, and direction of arrival (DOA) of acoustic rays from the transponders to the USV. Using a least-squares inversion, we show that DOAs improve single transponder positioning both in box-in and static acquisitions. From a series of short positioning sessions (20 min) over 2 days, we achieved a repeatability of ~5 cm in the locations of the transponders. Post-processing of the GNSS data also significantly improved the two-way-travel times residuals compared to the real-time solution.