An aquatic ecological evaluation of Calabar River Port terminals was carried out from February 2020 to January, 2021 with the aim of assessing seasonal variation of heavy metals and the distribution of phytoplankton. Atomic absorption spectroscopy (AAS) was employed to analyze heavy metal concentration and standard procedure was use in identification of phytoplankton from three sampling stations namely Eco marine terminal, INTELS terminal and Shoreline terminals in Calabar River port. Results showed elevated levels of lead, Chromium, Mercury, Zink, Nickel and copper in all the stations beyond the NESREA recommended limits. The study also showed significant negative relationship between plankton and heavy metals. It recommends a yearly monitoring by regulatory agencies to ensure that shipping activities do not interfere with water quality at the terminals.