Submarine groundwater discharge (SGD) is an important component of the hydrologic cycle connecting terrestrial to marine environments. SGD in fringing reefs and its consequences on biogeochemistry and ecology remain mostly unexplored. The 222Rn activity and salinity of seawater indicate a substantial groundwater contribution throughout most of the 20 km2 studied tropical reef in Pangasinan, Philippines. Over 30 km of electrical resistivity profiles with a penetration depth of 12.5 m shows widespread zones within the reef that are much more resistive than porous reef rocks or sediment saturated with typical seawater. Some discrete resistive areas are located close to where seawater has 222Rn peaks and where geologic lineaments are likely located suggesting that these are preferential pathways for fresher groundwater discharging to the reef. SGD at the site could be a major ecological factor connecting the reef to the subsurface environment which in turn may lead to connections to land.