Plant−bacterial associations can improve the degradation of various pollutants in soil. Bacterial root endophytes reside in a vast number of plant species as part of their root microbiome, with some being shown to positively influence plant growth. Wetland plant species with potential for phytoremediation possess various properties for degradation of wetland pollutants. Wetland soil or sediment environments have a number of physical, chemical, and biological consequences due to periodic or permanent flooding of soils and sediment. Plant roots release a broad variety of chemical compounds to attract and select microorganisms in the rhizosphere. They can form a complex micro-ecosystem and establish a dynamic balance with wetland plants to achieve a stable living space by colonization and rotating inside host plants. The composition of the root endophytic community has changed in response to increased levels of contaminants. However, little is known about the diversity and distribution of endophytic bacteria associated with aquatic plants and their potential to enhance phytoremediation of aquatic environment pollutants. This chapter summarizes the concept of endophytic bacteria, its role in phytoremediation, its distribution in roots, its functional diversity, and research methods.