Environmental pollution, encompassing a variety of contamination types such as air, water, and soil pollution, is a serious threat to both human health and ecosystems. To ensure a stable environment for habitation, immediate attention is necessary. Conventional methods face limitations, including complexity, high costs, waste disposal issues, use of harmful chemicals, and the need for heavy machinery and manpower, often resulting in toxic by-products. Bioremediation is an eco-friendly and effective approach, using biological agents like microbes and plants to eliminate or reduce the effects caused by contaminants. Genetic engineering and omics technologies represent sophisticated methods to manipulate these adaptable plants and microorganisms genetically or phenotypically, enhancing their capacity to draw out toxic substances from nature. This chapter explores major environmental pollutants and their removal using genetic engineering and omics approaches, showcasing examples and discussing their advantages and limitations.