Environmental microbiology plays a pivotal role in understanding how microorganisms contribute to ecosystem functions such as nutrient cycling, waste decomposition, symbiotic relationships, and climate regulation. This comprehensive review synthesizes current knowledge on the diversity and functional roles of microbes in soil and aquatic environments, as well as their interactions with other organisms and responses to human activities. We explore the contributions of soil microbes to nutrient cycling, highlighting processes involving carbon, nitrogen, phosphorus, and sulfur. The review also delves into aquatic microbiology, focusing on microbial roles in maintaining water quality and supporting biogeochemical cycles. The significance of symbiotic relationships in ecosystem stability and the dual role of microbes in greenhouse gas dynamics and climate regulation are examined. Furthermore, the review addresses the profound impacts of human activities on microbial ecosystems, including pollution, land use changes, and climate change, and discusses sustainable management practices to mitigate these effects. Technological advances in metagenomics, high-throughput sequencing, transcriptomics, proteomics, and bioinformatics have revolutionized the study of environmental microbiology, providing deeper insights into microbial diversity and functions. Finally, we outline challenges and future directions in the field, emphasizing the need for interdisciplinary approaches, advanced methodologies, long-term monitoring, and public engagement to protect and harness microbial ecosystems for environmental sustainability.