The growing concern of persistent organic pollutants in the environment causes hazardous effects on the ecosystem and living biota. Conventional strategies for cleaning organic pollutants, such as adsorption, advanced oxidation processes, membrane filtration, and photocatalysis, are expensive, inefficient, and generate secondary pollutants. Bioremediation is a cost-effective and eco-friendly means for environmental remediation. Microalgae are ubiquitous photosynthetic microorganisms offering sustainable environmental remediation, concomitantly producing high-value-added products and mitigating carbon emissions in a circular biorefinery framework. Integrating synthetic biology in microalgae-mediated bioremediation improves the efficacy of the process and minimizes the time. Molecular and genetic engineering advances have made it possible to rewire algal metabolic pathways to detoxify and mitigate the organic pollutants within the cellular systems. Further, the performance of natural communities can be tailored and enhanced using omics approaches and AI/ML tools, aiding in in situ remediation. This chapter explores the potential of different microalgal species for mitigating organic pollutants. Omics-based approaches for identifying target genes involved in the degradation mechanism and synthetic biology tools employed for enhancing bioremediation performance will be discussed.