The ability of endosymbiotic Symbiodinium to fix inorganic nutrients and their translocation to the coral host is considered a key element for the growth of coral reefs in tropical coastal waters and has been a fundamental research topic for over 50 years. With pulse-chase experiments using stable isotopes and combined TEM and NanoSIMS ultrastructural and isotopic analyses it is now possible to visualize and quantify the fixation, translocation, and turnover of essential elements such as carbon and nitrogen with unprecedented subcellular resolution. With these techniques we have monitored the assimilation of 15N nitrate, 15N ammonium, and 13C bicarbonate in the coral Pocillopora damicornis. These studies have revealed dynamic intra-symbiont storage of assimilated nitrate and ammonium in the form of uric acid crystals, and the formation of lipid droplets and starch granules in the symbiont and their subsequent remobilization. Carbon translocation toward the coral gastrodermal lipid droplets was detected within 15 min. Moreover, glycogen granules in the coral tissue were found to be an important sink for translocated carbon. This work has now been extended to the related pocilloporid species, Stylophora pistillata, with the important addition of heterotrophy (feeding the coral with dual-labelled brine shrimps) to contrast the fate and timeframes of heterotrophic vs. autotrophic (15N nitrate/13C bicarbonate) nutrient uptake under natural conditions and environmental stress due to elevated water temperatures. The in situ spatial data provided by NanoSIMS allow us for the first time to address questions that cannot be answered by traditional bulk measurements, such as 1) the influence of local symbiont densities on individual Symbiodinium assimilation rates, 2) metabolic capabilities of different symbiont ITS2 types in hospite, and (3) the effect of changes in intracellular host and symbiosome pH on individual symbiont productivity.