In the last decades an increasing number of natural and synthetic compounds have been recognized as endocrine disruptors (EDs) because of their hormone-like activity and capacity to alter the normal hormonal functions of animals and humans. Among EDs, there are phenolic compounds widely present in terrestrial and aquatic systems, such as bisphenol A, 4-nonylphenol (NP), 4-tert-octylphenol, estrone, ethynilestradiol and so on. Estrogenic effects of these molecules have been ascertained on mollusks, crustaceans, fishes, amphibians and mammals starting from concentrations of 1 μgL−1. Thus, the removal of EDs from polluted media is a priority goal in order to avoid risks for the ecosystem health. Nowadays, several physico-chemical methods are mainly used for the removal of EDs from liquid and solid matrices. Nevertheless, these methods are expensive, difficult to apply and may produce a negative impact on the environment. Recently, most of studies on soil and water remediation from EDs address more sustainable techniques using bacteria, fungi, microbial enzymes and plants. Phytoremediation uses photoautotrophic organisms to uptake, transform, volatilize or stabilize pollutants present in waters, sediments, soils and atmosphere. As this technology is solar driven and exploits natural sources, it is consequently environmentally safe and cost-effective. A fundamental role in the phytoremediation process is played by natural organic molecules, mainly dissolved organic matter and humic substances. These compounds are ubiquitous in all terrestrial and aquatic environments and they interact at various extent with all contaminants deriving from agricultural, industrial and urban activities. Natural organic matter has a relevant biological activity and may also regulate the decontamination capacity of plants and other organisms, such as algae and fungi. In this review, some results of phytodecontamination studies conducted using herbaceous plant species which are presented and discussed. Further, the modulation role of natural organic matter on the phytodecontamination process is highlighted.