Environmental microbiology of aquatic systems explores the intricate relationships between microorganisms and their aquatic habitats. These systems comprise diverse environments such as oceans, rivers, lakes, and wetlands, each hosting unique microbial communities crucial to ecosystem health. Microbes play pivotal roles in nutrient cycling, organic matter decomposition, and pollutant degradation, influencing water quality and ecosystem stability. Studying microbial diversity, community structure, and metabolic activities in aquatic environments helps elucidate their impact on global biogeochemical cycles and human welfare. Furthermore, environmental microbiologists investigate how natural and anthropogenic factors shape microbial communities, offering insights into ecosystem resilience and responses to environmental changes. This field's findings are pivotal for sustainable management and conservation efforts, highlighting the importance of microbial diversity in maintaining aquatic ecosystem function and resilience in the face of ongoing environmental challenges. This book elucidates new techniques and their applications in a multidisciplinary manner. The ever-growing need of advanced technology is the reason that has fueled the research in the field of environmental microbiology in recent times. This book will help new researchers by foregrounding their knowledge in the branch of environmental microbiology.