This study which was carried out between July 2019 and April 2020 aimed to determine the seasonal changes of heavy metals (Cd, Cr, Cu, Fe, Mn, Mo, Ni, Pb, Se, and Zn) in plant organs of Phragmites australis and Typha angustifolia grown in Eğirdir Lake and to research the usability of the these plants for phytoremediation with the calculation of bioaccumulation factor (BF). Plant samples were brought to the laboratory, and then washed, cleaned with distilled water, dried in an oven at 70 °C and acidified with 10 ml HNO3. The samples were heated at 120 °C on a hot plate until completely mineralized. After mineralization, heavy metal concentrations were determined by using ICP-AES (Vista model). Only Mo was the highest in leaf, while other metals were highest in root in P. australis. In T. angustifolia, Mn and Mo were highest in the leaf, the accumulation of other metals was observed to be higher in the plant’s roots than the other organs. It was discovered that the metal concentrations in root, in stem, and in leaf for both macrophytes generally increased in summer and decreased in root in autumn and winter and in stem and in leaf in spring for P. australis and in all organs in spring for T. angustifolia. Bioaccumulation factor (BF) values were calculated to determine the phytoremediation potential of P. australis and T. angustifolia. Both macrophytes are not excluder for all metals. Plants revealed potential for phytoremediation for the removal of heavy metals especially Mo and Zn. As a result of our study, it was determined that both macrophytes had accumulation abilities especially for Mo and Zn. It should be taken into consideration that these macrophytes can be used for improving the current situation of Eğirdir Lake due to their advantages such as being economical and not causing any harm to the environment.