The commercial vessels activity have a big role to increase the flow of number of cargoes from a port to another port. However, the impact of these activities are the disposal of ballast water from port area to the destination port. The purpose of this research was to analyze the correlation of phytoplankton, zooplankton, and heavy metal which were contained inside the ballast water of commercial vessel towards in waters of the port of Tanjung Emas Semarang. The concentration of heavy metal either from commercial vessels or the waters in port area analyzed by Atomic Absorption Spectrophotometer (AAS). The result showed that the correlation of zooplankton and phytoplankton in the water ballast at commercial vessels have a medium correlation to zooplankton and phytoplankton in waters of Port of Tanjung Emas Semarang (PTES) were 48.9% and 58.3%. Correlation of heavy metal Cd, Zn, Cu, Zn and Pb in ballast water of commercial vessel toward each metal in waters of PTES area has a strong correlation in contribution were 76.7%, 75.6%, 71.4% and 73.8%. It showed us that the loading activity of commercial vessels in port are contributed towards the pollution in waters.