This dataset contains data from the monitoring morphological evolution of beaches and coral reefs in Mayotte island. Mayotte, part of the coral reef-fringed Comoro archipelago in the SW Indian Ocean, experienced in 2018 and 2019 an intense seismic crisis. The repeated earthquake activity since May 2018 has been associated with deformation of the surface of Mayotte, resulting in land subsidence. The earlier 2006-2008 profiles were realized using a Leica TC 407® total station, and referenced to local IGN 50 benchmarks. The more recent 2019, 2020, and 2021 surveys were carried out using a GNSS differential Trimble R8S® system. Given the rapid subsidence that has affected Mayotte, the benchmarks used in this study, like others in Mayotte, need to be recalibrated by the IGN (French Institut Géographique National) and SHOM. This has still not yet been done, as the final outcome of the vertical island movements is still not clear.