Measurements of interstitial waters in deep wells (0 500 m) in Mururoa and in shallow bores (0 35 m) in Tikehau (French Polynesia) have shown high contents of dissolved nutrients and relatively low salinities, implying a deep oceanic origin. Studies of specific thermal fields within these atolls and carbonate platforms have led to models of deep oceanic water circulation by convection resulting from upward geothermal heat flow. Cold, low-salinity, low-pH, high-CO2, nutrient-rich deep oceanic water pervades the permeable atoll, where it loses density by heating related to geothermal heat flow, subsequently rising to seep out through the outer rim. New nutrients are thus continuously provided, enabling the reef-building community (algae+corals) to thrive in optimal conditions for photosynthesis and carbonate precipitation. This “geothermal endo-upwelling” concept is defined and its role in atoll trophic networks is emphasized as a necessary and sufficient process for reef net production and organic matter exportation. The endo-upwelled flow can then be viewed as a key factor for internal diagenesis, as early cementation of reef framework and dolomitization of deep limestone. Generalization of this interstitial, deep seawater circulation is discussed and linked to previously described thermal convection models in Florida or raised atolls.