Mayotte is located in the Mozambique Channel between Madagascar and Mozambique in the Indian Ocean, and is part of the Comoros archipelago. A hydro-sedimentary observatory was installed on three coastal catchment representative of the morphology, geology and land use observed on the island of Mayotte: the Mtsamboro catchment (19 ha), the Dzoumogné catchment (343 ha) and the Salim Be catchment (534 ha). For each watershed, the monitoring is composed of a hydrological and sedimentary station at the outlet and two climatic stations, located upstream and downstream of the basin. Rainfall, discharge and suspended sediment concentration data were recorded between November 2015 and August 2020 at 2-minute time steps. The data is available with a time step of one hour, one day and one month.