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Water flows from land to the ocean not only through rivers and estuaries but also below-ground through coastal and submarine aquifers. While the global fresh submarine groundwater discharge (SGD) is less than 1% of river discharge, it is quite relevant chemically as groundwater nutrient inputs are 25% of riverine inputs. This land-ocean connectivity is important for sensitive ecosystems such as coral reefs if the groundwater delivers solutes that are either critical for or harmful to reef life. Here, we present the interesting but potentially common situation of dramatic SGD in a volcanically active area in the Philippines which has been identified as the world’s most biodiverse coastal area and whose coral reefs provide for local communities. We studied coastal and submarine thermal springs associated with high fluxes of acidic waters and carbon dioxide, some of which are within or close to thriving coral reefs. The SGD fluxes are amongst the largest in the world and the SGD carbon dioxide fluxes overwhelm coastal carbon budgets. The presentation delivers explanations for the high SGD, discussing the mechanics and different sources and pathways of water, by bringing together multiple lines of evidence from different methods including deep diving, drones, novel sensors, geochemical tracers, thermal remote sensing, and modeling.