In recent years, red tides have posed severe threats to local economic development and ecological safety. Using real-time monitoring data from the Biogeochemical Argo from April to June 2019, we investigated the changes in the main ecological factors during red tide periods. The results led to the following conclusions: \mathrm{①} Water temperature began to increase from early spring and rose to about 20 °C in early May. Owing to the impact of river discharge and tidal current, surface salinity presents obvious daily fluctuations with a range of 22~31 PSU, which evidently decreases due to flooding. \mathrm{②} Dissolved Inorganic Nitrogen (DIN) and active phosphate are controlled by hydrodynamics prior to occurrence, whereas they are influenced mainly by algal growth and the supply of meteorological-scale flooding post occurrence. \mathrm{③} Nutrients and sea temperature are determined as key factors through Principal Component Analysis (PCA). Lastly, the variation in the ratio of N∶P and Dissolved Oxygen (DO) was further analyzed, and we proposed that the two chemical indices can be referred to as warning indices of red tide occurrence in Wenzhou Bay. This study will help build a linkage between red tides and hydrology and ecological factors, in support of forecasts and early warning of red tides.