In this dissertation, I aim to answer fundamental questions about the microbial interactions we share with built environments. I will begin in chapter two by addressing some of the most basic questions in built environment microbial ecology: where do the microbial communities originate, how unique are the communities associated with different residences, and how stable are these communities over time? In chapters 3 and 4; I will address how our microbial interactions with objects and built surfaces can potentially be leveraged for trace evidence in forensic investigations. Finally, in chapters 5 and 6, I will turn my focus to hospitals, the built environment whose microbial communities may have the most profound impact on human health and well being. Taken together, this work represents a great step forward in our understanding of the factors structuring microbial communities in built environments, and may provide insight into the design and usage of buildings in the future.