Submarine groundwater discharge (SGD) into a shallow lagoon on the west coast of Mauritius Island (Flic-en-Flac) was investigated using radioactive (3H, 222Rn, 223Ra, 224Ra, 226Ra, 228Ra) and stable (2H, 18O) isotopes and nutrients. SGD intercomparison exercises were carried out to validate the various approaches used to measure SGD including radium and radon measurements, seepage rate measurements using manual and automated meters, sediment bulk conductivity and salinity surveys. SGD measurements using benthic chambers placed on the floor of the Flic-en-Flac Lagoon showed discharge rates up to 500 cm/day. Large variability in SGD was observed over distances of a few meters, which were attributed to different geomorphological features. Deployments of automated seepage meters captured the spatial and temporal variability of SGD with a mean seepage rate of 10 cm/day. The stable isotopic composition of submarine waters was characterized by significant variability and heavy isotope enrichment and was used to predict the contribution of fresh terrestrially derived groundwater to SGD (range from a few % to almost 100%). The integrated SGD flux, estimated from seepage meters placed parallel to the shoreline, was 35 m3/m day, which was in reasonable agreement with results obtained from a hydrologic water balance calculation (26 m3/m day). SGD calculated from the radon inventory method using in situ radon measurements were between 5 and 56 m3/m per day. Low concentrations of radium isotopes observed in the lagoon water reflected the low abundance of U and Th in the basalt that makes up the island. High SGD rates contribute to high nutrients loading to the lagoon, potentially leading to eutrophication. Each of the applied methods yielded unique information about the character and magnitude of SGD. The results of the intercomparison studies have resulted a better understanding of groundwater–seawater interactions in coastal regions. Such information is an important pre-requisite for the protection and management of coastal freshwater resources.