The hydrographic characteristics and current circulation in Terengganu and Pahang coastal waters were examined for their spatial and temporal variability based on the seasonal influence during the transition period (April 2014) and southwest monsoon (June and August, 2014). The results of this study demonstrated the presence of slightly cooler water during June and August, 2014 compared to April, 2014, which indicate the existence of coastal upwelling. Furthermore, the uplifting of isotherms towards the coast during the study trip was also a good evidence of upwelling. The current flow generated by the wind was the possible reason of the features. Furthermore, this study also makes the first attempt to observe the coupling effects between coastal upwelling and the phytoplankton biomass in Terengganu and Pahang coastal waters, which is still sparse. Interestingly, apart from the nutrient availability, the coastal upwelling was believed to influence the phytoplankton biomass at the study area.