The study of geoid fluctuations in coastal areas is extremely important in understanding the changes in the extent of the Earth’s crust and also in the form of the mean sea surface topography (MSST). In recent years, the GNSS-on-boat method has made important steps towards the detailed description of marine topography, achieving precision to the order of a few centimeters, which is much more significant than has been achieved with the alternative satellite and altimetric methods. In this study, the method is applied for the first time in a lagoon, a challenging but exceptionally interesting environment both from a geophysical and hydrodynamic viewpoint. The ‘Papas’ lagoon in Western Achaia (Greece) was chosen for field measurements. The result for the geoid form shows a peak (13-15cm) in the marine topography approximately in the center of the lagoon. If this is confirmed in other lagoons or lakes, it will constitute a significant contribution to hydrocyanic dynamic models, which currently take as a basic assumption that the surface of the water is level. At the same time, the form of the SST indicates a significant reduction in gravity in the center of the lagoon, which may be linked either with a local reduction in the thickness-density of the Earth’s crust or with the existence of underground voids, faults or deposits.