<p>The marine transportation plays a pivotal role in the sustainable development of international logistics networks. The port water environment management has emerged as a key area of consensus with the proposal of green port world-wide. Nevertheless, the evolution of port water quality is always subject to various physical processes, the underlying mechanisms of which are complex. This study examines the spatiotemporal characteristics of water quality indicators in Zhanjiang Bay, China, from 2017 to 2024. Both statistical and correlation analysis methods have been employed to identify the most significant pollution factors and reveal the impact of vessel traffic flow and wind data on water quality subsequently. The results demonstrate that the deterioration of water quality was mainly caused by inorganic nitrogen (DIN) and reactive phosphate (DIP). The DIP content increased in the context of dense vessel traffic flow (<i>R</i> = 0.564, <i>ρ</i> = 0.015). A significant correlation was also observed between wind speed and DIN content (<i>R</i> = 0.500, <i>ρ</i> = 0.035). The impact of vessel traffic flow and wind data on the port water quality should be appropriately considered in the formulation of water environment management strategies.</p>