Microorganisms are ubiquitous and represent the vast majority of genetic diversity on the planet, driving critical ecosystem processes and influencing the evolutionary trajectories of many vertebrate species. Technological advancements in culture-independent molecular approaches have substantially increased our ability to identify and catalogue host-associated microbial communities. To illuminate key components in the natural history, overall biodiversity, and general health of wild animals, a more complete understanding of factors driving diversity and abundance of host-associated microbiota is necessary. In my dissertation research I present results from several extensive surveys of host-associated microbiota of migratory birds, focusing on how diversity and prevalence varies across time and geography. In Chapter 1, I examined the extent to which changing habitats impacted the within-individual composition of gut microbiota of a migratory habitat specialist, identifying habitat specific signatures in the microbiota. In Chapter 2, I characterized the microbiota of four species of widespread migratory birds on spring and fall migration as well as the start of the breeding season. Using observations replicated over three years, I found that microbial community diversity is significantly different across different periods of the annual cycle, and community composition is more similar within than across years. Third, I generated a dataset of avian malaria and malaria-like pathogens from migratory bird specimens collected during spring and fall migration over a 24-year time period. I used hierarchical statistical modeling to infer periodicity in pathogen prevalence and density-dependent disease modeling to explain plausible transmission mechanisms. The overarching results from this research demonstrate that significant and often recurrent shifts occur in host-associated microbiota throughout the annual cycle and over multi-year periods.