Under the backdrop of global warming, extreme weather events such as typhoons and storms are increasingly complicating the ecological processes in subtropical reservoirs. Based on five years of continuous monitoring data from 2019 to 2023 at Shanmei Reservoir in Fujian, we explored the response characteristics and mechanisms of algal blooms and high pH events to different rainfall-related meteorological conditions. The results show that algal blooms typically occurred from April to August, with filamentous cyanobacteria being the dominant species in terms of abundance. The maximum number of days per year with pH exceeding 9 reached 139, primarily occurring from April to August. The thermal stratification intensity in the euphotic layer (temperature difference per meter ≥ 0.20 °C), the number of non-rainy days within 7 days (fewer than 4 rainy days within 7 days), and total nitrogen (less than 1.80 mg/L) significantly contributed to the dominance of cyanobacterial abundance. Significant factors, including the thermal stratification intensity in the euphotic layer (temperature difference per meter ≥ 0.15 °C), the number of non-rain days within 7 days (more than 7 non-rain days) and total phosphorus (≥ 0.034 mg/L) were key to pH increase (higher than 9). These results reveal the intrinsic relationships between meteorological conditions, cyanobacteria, and pH, and identify the meteorological and environmental threshold values when cyanobacterial dominance occurs and pH exceeds 9, thereby providing scientific basis for developing water quality management and protection strategies for urban drinking-water reservoirs in the golden triangle of southern Fujian Province under future climate change scenarios.