Water quality evaluation in Lake Taihu, China, is vital for the regional water security. Recent studies have focused on understanding the spatio‐temporal dynamics of water conditions using long‐term data series. In this study, water conditions of Lake Taihu during non‐cyanobacterial/cyanobacterial growth periods were assessed based on water quality index (WQI), trophic level index (TLI), chlorophyll a concentration, and algal density; the spatio‐temporal changes in water quality were quantified, and their corresponding driving forces were discussed. The study employed water quality data from 2013 to 2018 and algal density data from 2013 to 2017. The results revealed that the water conditions varied over the years; it was the poorest in 2013, improved slightly in 2014, deteriorated during 2015–2017, and improved again in 2018. Slow algal growth was observed from May to July, which accelerated from August–September. The TLI in Lake Taihu may increase due to significant inflow during wet years, which may increase the eutrophication area and algae density in the following year, necessitating extreme caution. The northwestern part of Lake Taihu exhibited a lower WQI and higher TLI than its southeastern part. In the bays with high TLI, the WQI during the cyanobacterial growth period was lower than the non‐cyanobacterial growth period; the converse was observed in bays with low TLI. The results of this study imply that water conditions of Lake Taihu could be enhanced by reducing the nutrient load in wet seasons and wet years and improving the hydrodynamic conditions through water diversion, especially in Zhushan and Meiliang bays.