This paper presents the degree of heavy metals accumulation in existing Macrophytes in the water of the Bogota River to establish the potential of native species for the phytoremediation of contaminated aquatic ecosystems. The research was developed in four phases. The first one refers to the characterization of heavy metals in the water of the Bogota River in the study area; in the second phase it was determined the most abundant macrophytes species; in the third one, a preliminary determination of accumulation of heavy metals in the 3 dominant species using energy dispersive X-ray spectroscopy coupled to scanning electron microscopy (EDS-SEM) was then made. In the fourth phase, once it was selected the species with the greatest accumulation, an in vitro propagation under certain optimal nutrient conditions took place. Finally using a new measurement of EDS-SEM, it was determined the degree of accumulation of heavy metals. The results indicate that in the Bogota River, there are important concentrations of Zinc (Zn), Total Iron (Fe) and Chromium (Cr), which are associated with the industrial sector of the area. Also, it was determined that the most abundant species of macrophytes were Polygonum punctatum, Eichhornia crassipes and Myriophyllum aquaticum which showed characteristics of hyperaccumulating plants of Aluminum (Al) and Iron. Among them, Eichhornia crassipes stands out for its variety of accumulated metals, which is why, after the in vitro propagation and final analysis in EDS-SEM, it is concluded that it is an ideal species for phytoremediation of water bodies affected by iron, copper (Cu) and tin (Sn).