Bacteria are abundant in marine environments. They play important roles in nutrient cycling and form symbiotic interactions with eukaryotes. However, the vast majority of bacterial taxa are difficult to maintain in laboratory cultures, meaning that most microbiological research of the past century has focused on a small subset of bacteria. The advent of next generation sequencing (NGS) approaches, especially sequencing amplicons of the 16S rRNA gene, allowed researchers to detect bacteria in their natural environments, giving them the tools to conduct bacterial censuses and begin to understand how bacteria interact with their surroundings. Using 16S rRNA gene amplicon sequencing to describe the composition and structure of marine bacterial communities associated with animals residing in natural systems may provide vital indicators of health. However, if these animals reside in human-built environments, water treatment methods likely affect the composition of their bacterial communities, and conclusions drawn from researchers studying natural systems may not apply to those in a laboratory setting. Therefore, before conducting experiments on marine animals in a human built environment, it is crucial to understand how different water treatment approaches affect marine bacterial communities. If the effects of water treatment are not taken into account and/or standardized within the field of marine bacterial ecology, then experiments may be difficult to reproduce. This dissertation begins by describing the natural variation of the microbiome of the symbiotic intertidal sea anemone Anthopleura elegantissima. It then progresses to examine the microbiome of human-built systems, exploring how seawater treatment shapes the bacterial communities in a survey of the Hatfield Marine Science Center’s microbiome. Finally, it tests an ecological hypothesis put forth by those researching intensive aquaculture systems: that blooms of opportunistic pathogens can be suppressed by operating systems near their bacterial capacity to select against fast-growing taxa.