Ships transport about 80 percent of world trade and transfer approximately three to five billion tons of ballast water internationally every year. Due to the likely presence of pollutants, the ballast water discharged by ships can have negative effects on aquatic ecosystems. This study was conducted on 10 ships that entered the Bushehr port to determine the effectiveness of the ballast water exchange method and also to specify the contents of heavy metals (Ni, Cd, Pb and Cu) in the water and sediment of the ships’ ballast tanks. The samples were collected from January 2017 to July 2018 during a cold and a hot season. The results indicate the values of heavy metals in the samples in this order: Ni> Cu > Pb > Cd. The heavy metals concentrations in the sediment samples did not exceed the standard of the National Oceanic and Atmospheric Administration (NOAA). Whereas, Cu and Ni in all water samples and Cd in samples 2 and 7 exceeded the NOAA quality standard value. A correlation analysis of the metals showed that the sources of heavy metals vary in water and sediment samples, except for Pb and Cu in sediment samples which a positively significant relationship were observed. The results also revealed that the ballast water exchange method cannot by itself be effective and an efficient management together with continuous monitoring seems to be essential to prevent pollution of the ballast tanks of the ships entering the Bushehr port.