The release of organic compounds in the aquatic environment, resulting from different human activities, is a serious hazard due to the toxic, hydrophobic and persistent nature of these compounds. Removing organic contaminants from aquatic systems is vital and is one of the major topics of research in the arena of environmental science. Pesticides, plasticizers, pharmaceuticals, petroleum hydrocarbons are the organic pollutants which are considered to be the emerging contaminants of concern. Phytoremediation is a process of contaminant removal using plants, to clean up surface waters, groundwaters, sediments and soils. Phytoremediation of organic contaminants can occur through plant uptake, plant enzymes or exudates, or by the contribution of rhizosphere and endophytic organisms. Of all these, endophytic bacteria play a major role in contaminant removal. Endophytic bacteria occupy the interior tissues of plant without instigating adverse outcome or pathogenicity to their host. The endophytic bacteria exhibiting contaminant degradation and growth-promoting activities in plants are meant for better phytoremediation. Also, recently wetlands have been anticipated as places for phytoremediation of contaminants. This review summarizes the activity and ability of endophytic bacteria of wetland plants to augment the competent process of phytoremediation of organic contaminants in water and discusses the mechanism followed by endophytic bacteria to enhance phytoremediation of organic contaminants. Understanding the mechanisms behind endophytic bacteria and wetland plant interaction is necessary to meet the complete biotechnological know-how of bacterial-plant associations for various uses.