Introduction: Typhoons can strongly perturb coastal biogeochemical processes, yet the timing of nutrient–phytoplankton responses remains poorly resolved in eutrophic semi-enclosed bays. This study investigated the stage-dependent physical, chemical, and biological responses of Zhanjiang Bay during Typhoon Sanba in October 2023.

Methods: High-frequency in situ observations of hydrometeorological conditions, salinity, dissolved oxygen, pH, dissolved inorganic nutrients, and chlorophyll-a (Chl-a) were divided into pre-typhoon, typhoon-disturbance, and post-typhoon recovery stages. Stage differences were assessed using non-parametric tests, and Spearman correlations were used to evaluate changes in Chl-a–environment relationships. A complementary long short-term memory (LSTM) model was developed using a longer hourly dataset to assess the predictability of smoothed Chl-a variability.

Results: Strong wind forcing, heavy rainfall, and freshwater input caused rapid freshening and substantial nutrient enrichment. Median dissolved inorganic nitrogen increased from 0.609 to 1.199 mg N L⁻¹, while dissolved inorganic phosphorus increased from 0.054 to 0.087 mg P L⁻¹. However, Chl-a did not increase synchronously during peak disturbance and showed no significant correlations with the measured environmental variables, indicating temporary decoupling between nutrient enrichment and phytoplankton biomass. After physical forcing weakened, Chl-a increased markedly, with peaks approaching 18 μg L⁻¹, and became positively associated with water temperature, dissolved oxygen, pH, and dissolved inorganic phosphorus. The LSTM model reproduced smoothed Chl-a variability with an RMSE of 2.13 μg L⁻¹, an MAE of 0.89 μg L⁻¹, and an R² of 0.94.

Conclusions: The main biological response emerged after typhoon passage, demonstrating disturbance-driven decoupling followed by recovery-stage recoupling. Extended post-event monitoring is therefore essential for detecting delayed phytoplankton amplification and assessing bloom risk in eutrophic semi-enclosed bays.