Submarine groundwater discharge (SGD) is widely acknowledged as a key driver of environmental change in tropical island coral reefs. Previous work addressed SGD and groundwater-reef interactions at isolated submarine springs; however, there are still many outstanding questions about the mechanisms and distribution of groundwater discharge to reefs. To understand how groundwater migrates to reefs, we performed a series of offshore 222Rn (radon) and submarine electrical resistivity (ER) surveys on the tropical volcanic island of Mo’orea, French Polynesia. These surveys suggest that fresher water underlies the fringing reef, apparently confined by a <1 m thick low-permeability layer referred to as a reef flat plate. Reef flat plates have been documented elsewhere in tropical reefs as thin, laterally continuous limestone units that form through the super-saturation of calcium carbonate in the overlying marine waters. In other tropical reefs, the reef flat plate is underlain by a highly permeable karstic limestone formation, but the submarine reef geology on Mo’orea is still uncertain. Numerical modeling of 2D reef transects and SGD quantifications based on water budget and radon/salinity mass balance support the confining nature of the reef flat plates and indicate important implications for SGD impacts to tropical reefs. Except where incised by streams or local springs, reef flat plates may route SGD to lagoons or to the reef crest 100s of meters offshore. Because groundwater can transport pollutants, nutrients, and low pH waters, the reef flat plate may play an important role in the spatial patterns of reef ecology and coastal acidification.