Metagenomics has emerged as a powerful tool in environmental monitoring, offering novel insights into the composition, diversity, and functional potential of microbial communities across diverse ecosystems. This chapter explores the integration of metagenomics with multi-omics approaches—such as genomics, transcriptomics, and proteomics—highlighting their synergistic contributions to a deeper understanding of ecosystem processes. The application of advanced technologies, including high-throughput sequencing and single-cell genomics, has significantly accelerated the characterization of environmental microbiomes, thereby enabling more precise and dynamic ecological assessments. In the context of global challenges, such as climate change, metagenomics serves as a critical approach for evaluating ecosystem resilience and elucidating the role of microbial communities in biogeochemical cycles, particularly carbon and nutrient fluxes under environmental stress. Microbial consortia have shown remarkable abilities to degrade both organic and inorganic contaminants, thus playing a significant role in bioremediation and ecological restoration. The growing adoption of environmental DNA (eDNA) techniques has further enhanced biodiversity assessments, enabling real-time, non-invasive monitoring of species and ecosystem health. This chapter also examines the utility of metagenomics in detecting emerging pollutants and tracking antimicrobial resistance genes—factors that are pivotal for both environmental stability and public health. The incorporation of machine learning (ML) and artificial intelligence (AI) has improved the processing and interpretation of complex metagenomic datasets, thereby fostering greater analytical precision. Additionally, the role of metagenomics in informing environmental policies and supporting progress toward the United Nations Sustainable Development Goals (SDGs) is emphasized. Overall, this chapter positions metagenomics as a cornerstone of modern ecological research, essential for evidence-based decision-making and effective management of global environmental challenges.