Microbes, simple single-cell organisms, are the oldest living inhabitants of the world and are believed to be present everywhere, from the deepest ocean trenches to the clouds above our heads. Human bodies harbor a diverse ensemble of microbial communities across their various environmental niches, mirroring the diversity of our home world. Human-associated bacteria disperse from their host bodies into the environment through daily activities. Given that modern humans spend up to 90% of their time indoors, it is unsurprising that indoor spaces are teeming with human-associated bacteria, detectable on surfaces, dust, and even in the air. Surfaces exposed to human contact are routinely utilized in forensic science to uphold the law; these surfaces serve as valuable sources of information. This thesis showcases how microbial signatures detected on indoor surfaces can be leveraged to monitor the health of residents and identify potential risks to human health. Chapter 1 sets the stage by exploring the microbial and chemical exposures experienced by humans while living indoors. It introduces key experimental techniques such as surface swabs, multiple data layers, and three-dimensional data visualization, which will be used throughout the thesis. Additionally, given the backdrop of a global pandemic, Chapters 2 and 3 focus on developing and deploying surface swabbing techniques to enhance environmental monitoring support for the COVID-19 pandemic response. Finally, Chapter 4 presents the culmination of this research, utilizing surface swabbing in the International Space Station to create the most extensive microbial and chemical map of an indoor space habitat to date, shedding light on the potential challenges of long-term human space habitation.