Knowledge of the position and motion of points on the seafloor can be critically important in both fundamental research (for example, global geodesy and plate tectonics) and for more practical applications such as seismic risk evaluation, off-shore construction and pipeline monitoring. In the Vanuatu subduction zone, for example, measuring deformation underwater could provide valuable information for modeling deformation and understanding the seismic cycle. We report a shallow water experiment in Vanuatu to measure the relative and absolute depth of seafloor points. The experiment differs from previous efforts mainly in that it uses the height of the sea surface determined by kinematic GPS, allowing us to locate the points in a global reference frame. The ITRF2005 ellipsoidal height of a seafloor benchmark was determined with a 1-sigma uncertainty of 0.7–2.1 cm. The estimated ellipsoidal height differs only by a few tenths of a centimeter between measurements made in 2004 and another set made in 2006. These results are encouraging and open new perspectives for vertical underwater deformation monitoring in shallow water areas. Sea-surface GPS measurements can also help to reduce the uncertainty in depth difference determination for relative measurements.