The aim of this study was to investigate the concentrations and pollution levels of heavy metals, organochlorine pesticides, and polycyclic aromatic hydrocarbons in marine sediments from the Leghorn Harbor (Italy) on the Mediterranean Sea. The phytoextraction capacity of three aquatic plants Salvinia natans, Vallisneria spiralis, and Cabomba aquatica was also tested in the removal of lead and copper, present in high concentration in these sediments. The average detectable concentrations of metals accumulated by the plants in the studied area were as follows: >3.328 ± 0.032 mg/kg dry weight (DW) of Pb and 2.641 ± 0.014 mg/kg DW of Cu for S. natans, >3.107 ± 0.034 g/kg DW for V. spiralis, and >2.400 ± 0.029 mg/kg DW for C. aquatica. The occurrence of pesticides was also analyzed in the sediment sample by gas chromatography coupled with mass spectrometry (GC/MS). Due to its metal and organic compound accumulation patterns, S. natans is a potential candidate in phytoextraction strategies.