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Abstract Due to the blockage of seawater, seafloor displacement cannot be directly measured by space geodesy. The combination of Global Navigation Satellite Systems‐acoustic ranging (GNSS‐A) has been used to overcome the electromagnetic barrier, so that a GNSS‐determined sea surface vessel's coordinates can be transformed to seafloor benchmarks in a global reference frame. Due to the high cost and science priorities, previous GNSS‐A studies mainly targeted relatively deep water and a minimum of three transponders were used to form an array, equivalent to a precision geodetic station. With recent developments in unmanned autonomous surface vessels, low cost GNSS‐A surveys are poised to become practical. Here we demonstrate that with a carefully designed surveying trajectory, Wave Glider‐based GNSS‐A surveying of a single transponder in shallow water can provide centimeter‐level accuracy on horizontal seafloor positioning, even if the sound speed model deviates from the actual value by a few meters per second. Results from a nine‐month experiment conducted at ∼54 m water depth show that the repeatability of the seafloor horizontal positioning is better than 2 cm. When conditions allow, the acoustic observations should be collected symmetrically about the transponder and data redundancies are recommended to reduce the error associated with time‐dependent variations in sound speed.