Measuring seafloor motion in shallow coastal water is challenging due to strong and highly variable oceanographic effects. Such measurements are potentially useful for monitoring near‐shore coastal subsidence, subsidence due to petroleum withdrawal, strain accumulation/release processes in subduction zones and submerged volcanoes, and certain freshwater applications, such as volcano deformation in caldera‐hosted lakes. We have developed a seafloor geodesy system for this environment based on an anchored spar buoy topped by high‐precision GPS. Orientation of the buoy is measured using a digital compass that provides heading, pitch, and roll information. The combined orientation and GPS tracking data are used to recover the three‐dimensional position of the seafloor marker (anchor). A test system has been deployed in Tampa Bay, Florida, for over 1 year and has weathered several major storms without incident. Even in the presence of strong tidal currents which can deflect the top of the buoy several meters from vertical, daily repeatability in the corrected three‐component position estimates for the anchor is 1–2 cm or better.