Aquatic plants are vital for improving water quality and promoting sustainable aquatic ecosystem management through natural phytoremediation. The present article summarizes the roles of emergent, floating, and submerged macrophytes in removing excess nutrients, trapping suspended solids, enhancing dissolved oxygen, supporting beneficial microorganisms, and sequestering heavy metals. Species such as Eichhornia crassipes, Pistia stratiotes, Ipomoea aquatica, Lemna spp., and Azolla spp. effectively reduce pollutants from aquaculture effluents and wastewater. Their integration into aquaculture systems improves water quality, lowers disease risks and operational costs, and produces valuable biomass for feed, fertilizer, and bioenergy. The article also highlights their application in Recirculating Aquaculture Systems (RAS) and Integrated Multi-Trophic Aquaculture (IMTA), emphasizing careful species management to maximize environmental sustainability and support the blue economy.