Aquatic systems hold a major portion of the Earth’s crust, providing a natural habitat to life. There is a strong network among microbes, cyanobacteria, and plants, giving birth to a complex ecosystem in the water bodies, which directly and/or indirectly affects countless other species related to the aquatic system. This delicate system is being affected by aquatic pollution; however, their interaction has emerged as a promising aspect for the treatment of ecosystems and strengthening the stability of the ecosystem. Human activities are destroying these natural ecosystems by adding pollutants from various sources including heavy metals, organic compounds, nutrients, fertilizer runoff, and municipal wastewater. These effluents cause major disruption in the ecosystem, sometimes causing it to collapse. Different techniques including physical and chemical approaches have been applied to ensure the cleanliness and maintenance of these ecosystems, but usage of these technologies is limited due to restricting factors including high cost, sustainability, and efficiency. Aquatic plant species remove effluents from water systems by phytoextraction, phytostabilization, and rhizofiltration. Different types of mutualistic relationships can also help in better treatment of the water bodies because plant roots provide shelter to many microbes like bacteria and fungi. These microbes help in reduction and uptake of unwanted or extra nutrients thereby saving the environment from deadly blooms. This chapter focuses on phytotechnologies such as phytoremediationPhytoremediation, phytostabilization, and phytotransformation and to assesse the most effective system among all. Different plants species have different biodegradation and phytoextraction abilities, their extent is explored in this chapter, where selection of the specific species for specific purposes by checking their nutritional needs and environmental conditions for maximum output is emphasized. Phytotechnologies and their use highlight an eco-friendly and sustainable system for the treatment of contaminated systems, while their implementation requires complete knowledge about species selection, pollutants, site conditions, and management strategies.