Environmental pollution, driven by industrialization and urbanization, presents severe challenges to ecosystems, biodiversity, and human health. Bioremediation, leveraging microorganisms and plants to mitigate pollutant impacts, has emerged as a promising solution due to its cost-effectiveness and environmental sustainability. This chapter highlights recent advancements in metagenomics, an innovative approach that analyzes genetic material from environmental samples, providing insights into microbial diversity and functionality. By enabling the detection of novel genes, pathways, and enzymes associated with pollutant degradation, metagenomics enhances our understanding of microbial interactions with contaminants. Cutting-edge sequencing technologies alongside bioinformatics tools are pivotal in elucidating microbial community dynamics and optimizing bioremediation processes. Case studies reveal metagenomics’ potential to identify pollutant sources, develop targeted remediation strategies, and monitor environmental recovery. The integration of metagenomics with proteomics and transcriptomics represents a paradigm shift, enabling sustainable solutions for environmental remediation. This study underscores the need for continued exploration of microbial potential to address emerging pollution challenges and ensure ecological resilience.