Eco-friendly and cost-effective biotechnological approaches such as phytoremediation are gaining prominence in restoring polluted water bodies containing excessive pollutants in the form of heavy metals, pesticides, and excess nutrients. Phytoremediation incorporates the natural ability of the plants to absorb, accumulate, degrade, or stabilize the pollutants from aquatic environments. Aquatic macrophytes such as Eichhornia crassipes (water hyacinth), Typha latifolia (cattails), and Lemna minor (duckweed) play a significant role with their high biomass, fast growth, and capacities for pollutant uptake. New breakthroughs in genetic engineering and microbial symbiosis have improved the phytoremediation potential of plants through increased resistance to contaminants and increased pollutant removal efficiency. Despite potential vastness, problems that exist include those of disposal of plants at the end of the process, efficiency at certain times of the year, and location-specific constraints. This chapter discusses, in relation to rehabilitating contaminated water bodies, the mechanisms involved in phytoremediation that include phytoextraction, rhizofiltration, and phytodegradation and then points to its integration with sustainable water management approaches for long-term environmental restoration and ecosystem health.