As industrialization evolves, it is accompanied by vast utilization of natural resources and synthetic compounds which often results in nature distortion and consequently poses heavy environmental concerns. The rigorous search for sustainable solutions to these issues paved the way for the emergence of an affordable, safe, and eco-friendly plant-based approach, widely known as phytoremediation, which has proven to be potent in getting rid of toxic environmental contaminants and pollutants such as radioactive compounds, pharmaceuticals, xenobiotics, pesticides, oil spills, heavy metals, and medical wastes. Further insights into phytoremediation at the genetic level have been gained and advanced via omics technologies. This chapter explores diverse omics technologies including metabolomics, genomics, metaproteomics, phenomics transcriptomics, signalomics, proteomics, metagenomics, fluxomics, meta-transcriptomics, and metabolomics highlighting their integration, recent developments, limitations, and future perspectives toward improving the effectiveness of plants for higher phytoremediation efficiency and sustainable wastewater treatment endeavors. Recent technological efforts and advances toward the discovery of plant biosynthetic pathways via omics technologies and integration avail new paths and opportunities. Proteome-based methods have also been more vastly explored in plant pathology studies, and tracking of phosphorylation alterations in enhancing signal transduction pathways identification and protein function, while metabolomics and transcriptomics have helped understand mechanisms underlying phytoremediation, identify emerging plant biosynthetic pathway members, and also target specific ones.