Corals combine photosynthesis and calcification in an intricate and delicately balanced relationship to form large biomineralized structures that are dominant features of tropical coastlines worldwide. Coral reefs have great scientific and economic importance but have recently experienced widespread decline attributed to increasing anthropogenic pressure on reef systems. Physical damage events, such as ship groundings, when coupled with existing nutrient stress and changing global climate present a poor outlook for successful natural recovery of reef communities. The main goal of the proposed research is to better understand how environmental factors, both local and global, affect the coral holobiont and influence overall coral fitness. The target species of this research, Montastraea cavernosa and Porites astreoides, are important and widespread Caribbean reef-builders. While it has been shown that nutrient and pCO2 stress affect coral growth and calcification, study of specific effects on coral tissue and reproductive success has not received significant attention in the literature despite considerable current interest. This study addresses this data gap in quantitatively examining the effect of elevated nutrients and pCO2 on 1) P. astreoides recruit survivorship, development, early calcification, and symbiotic zooxanthellae morphology; 2) M. cavernosa and P. astreoides wound regeneration, tissue characteristics over time at the histological and ultrastructural level, and trends in symbiotic zooxanthellae morphology; and 3) survival, growth and histological/ultrastructural characteristics of M. cavernosa and P. astreoides fragments transplanted to the field and in the laboratory. Histological and ultrastructural observations from corals transplanted to the field are then compared to ex-situ laboratory experimental corals. In the fleshy and large-polyped faviid M. cavernosa, healing of a linear wound was characterized by granulation of new tissue across the wound site, facilitated by coalescent granular amoebocytes. The wound healing strategy of this species appears to progress with wound closure and re-epithelialization before calcification resumes, as actively calcifying calicodermis was generally not observed at the healing front. Tissue regeneration in the small-polyped P. astreoides was characterized by formation of multiple islands of eosinophilic healing fronts along the depth of the wound track, and an accumulation of granular amoebocyte cells in regenerating tissue. The wound healing strategy of this species appeared to result in re-epithelialization of exposed body wall without necessarily closing the wound. Elevated pCO2 significantly reduced survivorship in P. astreoides recruits, and both nutrient enrichment and elevated pCO2 significantly reduced wound regeneration rate in M. cavernosa and P. astreoides. In both species, phosphate enrichment had the greatest deleterious effect on wound repair. A significant application of this study is the identification of possible zooxanthellar morphological indices of elevated nutrients and ocean acidification. The similarity in starch, lipid and uric acid accumulation patterns in Symbiodinium sp. from P. astreoides recruits and coral fragments of both species indicate a correlation between these anthropogenic stressors and the intracellular accumulation of excess carbon and nitrogen by the symbiont. Zooxanthellar carbon accumulation, in the form of starch and/or lipid, was the greatest under elevated nitrate. Zooxanthellar nitrogen accumulation, in the form of uric acid, was the greatest under elevated CO2. Comparison of zooxanthellar metrics between the field corals (P. astreoides, and M. cavernosa) and ex-situ corals and recruits indicated that carbon accumulation in Symbiodinium from field corals was consistently significantly less than in the ex-situ experimental P. astreoides recruits and M. cavernosa fragments exposed to elevated nitrate. This indicates that the field corals were likely not exposed to elevated nitrate at the time of collection. Both M. cavernosa and P. astreoides adults in the field accumulated significantly less uric acid than their counterparts in the tissue repair experiment, indicating that the field corals were exposed to higher pH and lower CO2 than the ex-situ corals. These results suggest that the field corals were not exposed to nutrient concentration profiles similar to the experimental treatments, particularly elevated nitrate. However, histological metrics indicated that the transplanted corals were subjected to increasing sedimentation stress over time. Overall, nitrate was found to affect recruits and adults on a similar scale, while phosphate and pCO2 affected carbon and nitrogen storage more in recruits compared to adults. While nutrients and pCO2 had no mechanistic effect on regeneration at histological level, ultrastructural metrics indicate an impact on the mutualistic energy exchange between the symbiotic partners, partially decoupling symbiosis. Effects were generally found to be greater in P. astreoides compared to M. cavernosa, and the unique life history strategy of the subject species and differences in their endosymbiont physiology reveal distinct responses to elevated nutrients and pCO2. Although the laboratory findings were not necessarily applicable to field observations, they provide insight into factors that may influence fragment success in the field. Quantitative assessment of the effect of elevated nutrients and pCO2 is thus useful in management decisions involving water quality standards, and is essential in the prediction of future coral condition and resilience.