Abstract: Rationale The functioning of mangrove forests found on small coralline islands is characterized by limited freshwater inputs. Here, we present data on the water cycling of such systems located on Europa and Juan de Nova Islands, Mozambique Channel. Methods In order to better understand the water cycle and mangrove growth conditions, we have analysed the hydrological and salinity dynamics of the systems by gauge pressure and isotopic tracing (δ18O and δ2H values). Results Both islands have important seawater intrusion as measured by the water level change and the high salinities in the karstic ponds. Europa Island displays higher salinity stress, with its inner lagoon, but presents a pluri-specific mangrove species formation ranging from shrub to forest stands. No freshwater signal could be detected around the mangrove trees. On Juan de Nova Island, the presence of sand and detrital sediment allows the storage of some amount of rainfall to form a brackish groundwater. The mangrove surface area is very limited with only small mono-specific stands being present in karstic depression. Conclusions On the drier Europa Island, the salinity of all the water points is equal to or higher than that of the seawater, and on Juan de Nova the groundwater salinity is lower (5 to 20 PSU). This preliminary study shows that the karstic pothole mangroves exist due to the sea connection through the fractured coral and the high tidal dynamics. Copyright © 2015 John Wiley & Sons, Ltd.