Metabolic rate refers to the rate by which chemical energy is converted into biological energy and used for either maintenance of existing structure or production of new biomass. The Metabolic Theory of Ecology (MTE) predicts the metabolic rate of individual organisms based on the observation that most variation in an individual's metabolic rate can be explained by body size and temperature. The objective of this dissertation was to investigate the bioenergetics of coral reef systems using MTE. My hypothesis was that human activities alter the energy budget of the reef system, specifically by altering the allocation of metabolic energy between microbes and macrobes. I found that in reef systems, even a small increase in microbial biomass can result in substantial changes in whole system rates of energy and materials flux. By comparison, relatively large reductions in fish biomass, affect the system bioenergetics to a lesser degree. The percentage of the combined fish and microbial predicted metabolic rate that is microbial, a.k.a. the microbialization score, was used as a metric for assessing and comparing reef health. My results demonstrated a strong positive correlation between reef microbialization scores and human impact. Regardless of oceanographic context, the microbialization score was a powerful metric for assessing the level of human impact a reef system is experiencing. The process of microbialization was further examined by assessing the effects of human activity on the relative roles of heterotrophic and autotrophic microbes. I found that shifts in microbial trophic structure change both the magnitude and efficiency of energy flow. Specifically, there was a significant increase in the ratio of autotrophic to heterotrophic microbes with human impact, which was also related to an increase in the mass specific energy requirements (W g-1) of the microbial community. I am proposing that microbialization is actually a mechanism of reef resilience that dampens the effects of both overfishing and eutrophication. In conclusion, this research sheds new light on the effects that rising human impact has on the bioenergetics of coral reef systems and adds to our current understanding of the mechanism(s) that underlie reef system degradation.