Reef-building corals provide essential ecosystem services to people. Unfortunately, anthropogenic activities, such as overfishing, coastal pollution and global climate change threaten reef survival. Given recent declines in coral reefs, researchers need new tools to cheaply and quickly evaluate coral metabolic states to assess reef health and describe mechanisms linked to coral stress responses. This dissertation develops a broader understanding of coral-algal symbioses and holobiont response to disturbance events by applying metabolomic tools to corals. Metabolites are small compounds that are products and intermediates of cellular metabolism; as such they support individual physiology, reproduction, and survival. To assess the utility of metabolomics for reef corals, I developed a proton-nuclear magnetic resonance (1H-NMR) metabolomic approach that can reproducibly detect biologically relevant compounds and find significant differences among species. These data indicate 1H-NMR metabolomic techniques can profile coral metabolomes and provide an integrated picture of coral phenotypes in response to environmental change. Therefore, to explore shifts in coral metabolomes as a function of environmental stress, I exposed replicate colonies of Pocillopora damicornis to current and future temperature and pCO2 conditions for 1.5 months. I collected primary metabolite and lipid profiles using mass spectrometry (MS) to investigate shifts in cellular metabolism after prolonged exposure to treatment conditions. Metabolomes shift in response to treatments and therefore indicate corals alter metabolic pathways to maintain cellular homeostasis. However, not all corals respond equally to ecological disturbances and their response is dependent on the symbiosis between corals and Symbiodinium. To determine if coral associated Symbiodinium communities relate to metabolite composition, I collected 1H-NMR profiles and Symbiodinium community data from nine different coral species. These data indicate metabolite profiles correlate to symbiont composition and can predict different levels Symbiodinium diversity. Furthermore, Symbiodinium-metabolite correlation networks reveal functional variation in coral symbiont communities in hospite. Taken together, this dissertation illustrates the power, utility, and feasibility of implementing metabolomic tools to characterize coral metabolic status. Metabolomics can help describe mechanisms underlying changes in coral physiology, which can help ameliorate stress on reefs and identify the biological consequences of anthropogenic disturbances.