One of the most pressing environmental issues worldwide today is heavy metal pollution. This study aimed at isolating endophytic bacteria from the internal cells of the roots, stems, and leaves of Lemna gibba and Eichhornia crassipes collected from a permanent pond in the Nile Delta, to remove various heavy metals (Cu, Cr, and Pb). Of the 44 total isolates, 34 isolates were considered positive for exopolysaccharides. The halotolerance test revealed that all the isolates tolerated NaCl stress up to 15%, and when the bacteria were stressed by growth in 20% and 25% NaCl, 21 and 17, respectively, were able to grow. The growth kinetics of the isolates were examined with Pb and Cr metal (150 and 300 mg L-1) independently. To estimate the Pb ion minimum inhibitory concentration, four Pb-tolerant bacterial isolates were chosen. The isolates were grown in LB medium with 100-500 mg L-1 Pb metal ions and measured at 600 nm at predetermined time intervals (8, 12, 24, 48, and 72 h). All bacterial stains survived 100–500 ppm lead concentrations. In this work, the effectiveness of a single isolate, 2Pe, in removing Pb was evaluated. At an ion concentration of 20 mgL-1, isolate (2Pe) removal efficiency was 21.65%. The endophytic isolate (2Pe) was described morphologically and biochemically, and its name was identified by 16S rRNA sequencing. In the end, humans, animals, plants, and everything else in the ecosystem are all put under stress by the accumulation of heavy metals in the environment. To ensure efficient and cost-effective procedures, it is necessary to have a thorough awareness of the process and the available options for remediation at each stage.