Coastal oceans are highly responsive to typhoons, making them one of the most affected regions. However, our understanding of the impact of typhoon intensity and movement path on marine dynamic processes and eco-environmental factors remains limited because there are very few on-site investigations, especially continuous field observations in the bay during typhoon events. This study investigated dual water isotopes through a continuous survey (with a 5-day interval) during ten cruises in Zhanjiang Bay, associated with two typhoons of varying intensities and landing tracks (left and right sides). After typhoons, the water mass mixing intensified and lasted for several weeks, depending on the intensity of typhoons. During the typhoon periods, there was a considerable increase in contributions from freshwater to nutrient loads; however, this contribution was higher from the stronger typhoon than the weaker one. The weaker Typhoon Lionrock, which landed on the left side of the bay, enhanced the ocean front due to onshore winds induced by the typhoon, causing intrusion of high-salinity seawater into the bay and retaining pollutants in the bay. However, when stronger Typhoon Chaba landed on the right side, offshore winds induced by counterclockwise wind stress during the typhoon resulted in more seawater flowing toward the lower and outer bay. This prevented the forming of an ocean front and played a dilution role in pollutants through its hydrodynamic process. This was primarily due to the fact that the landing trajectory of typhoons directly influenced the direction of seawater flow in Zhanjiang Bay, while the intensity of typhoons further amplifies these flow patterns. This study suggests that tracks of typhoon movement, rather than their intensity and terrestrial runoff, play a crucial role in governing marine dynamics and nutrient supplies in coastal bays during typhoon events.