Microorganisms provide essential services for host organisms and this is especially true for communities of algal symbionts and bacteria hosted by tropical reef-building corals–collectively termed the coral holobiont. Endosymbiotic algae provide essential nutrients to the host, and can impact coral growth and susceptibility to environmental stress. Corals also associate with a diverse microbiome, and specific bacterial taxa have been implicated in important nutritional and immunity roles. However, fundamental questions regarding the environmental factors that govern coral holobiont composition remain unanswered. The overarching goal of my dissertation is to characterize how environmental variation, including disturbance, influences the composition of coral-associated algal and bacterial communities. To achieve this goal, I first compared these communities across reef zones (locales differing in diel thermal variability and other factors) in tandem with host genetic background under baseline conditions. I found that in the more stable reef zone, algal communities were more diverse and that host genetic diversity correlated with bacterial diversity, implying the more variable reef zone constrained diversity of host-microbial partnerships. Next, I characterized how these communities responded to a hurricane disturbance in two stress-tolerant congeneric coral species. Again, I observed stark differences across reef zones in algal symbiont and bacterial communities, but these communities were not exceptionally impacted by disturbance. Finally, I experimentally tested the role of daily thermal variability as a key environmental factor in shaping holobiont community composition and heat tolerance. While thermal variation treatment increased algal photosynthetic efficiency, it did not facilitate coral thermal tolerance to heat stress. Specific bacterial taxa were differentially abundant after 90 days in treatment acclimation, suggesting that thermal variation may contribute to part of the observed community differences across natural reef zones. In sum, this dissertation provides a deeper understanding of the interplay between coral-associated microorganisms and their local reef environments, as well as taxa-specific patterns of interest for monitoring coral holobiont dynamics under rapidly changing oceans.