Detailed hydrographic survey revealed patches of high nutrients and low salinity in the surface waters over a submerged limestone barrier reef in the oligotrophic coastal waters of the southeast Indian Ocean. The nutrient patches exist throughout the year and represent concentrations that are more than 10 times those in the surrounding water. Numerical model results show that the nutrients originate from the reef and that the patchiness is caused by changes in water circulation. The limestone in the region is known to be solution riddled, and submarine seeps of nutrient-rich groundwater on the reef are a likely source. Underground conduits represent major routes by which groundwater nutrients can be transported over several kilometers and supplied to barrier reef ecosystems, resulting in "islands" of high productivity.