The water quality of Lake Chaohu has improved significantly from the mid-1990s to 2012. But in recent years, water quality improvement has slowed down. In particular, cyanobacterial blooms area increased significantly in 2018. In order to evaluate the variation of water environment, we analysed the change characteristics of water quality and cyanobacterial blooms situation in Lake Chaohu using the investigation data covering 17 sites from 2012 to 2018. We also elaborated the progress and shortcomings of water pollution control in Lake Chaohu in the spatial scale of the basin, which will provide support to the modification and confirmation of pollution control policy. Our results showed that the mean values of total phosphorus concentration, total nitrogen concentration and bloom-forming cyanobacterial biomass (chlorophyll-a and phycocyanin concentration) increased significantly from 2012 to 2018, and the ammonia nitrogen concentration decreased significantly during this period. In spatial, the eutrophication presented slight decreasing trend in the western region, but it significantly increased in the central and eastern regions, especially for the total phosphorus concentration. Even though, the eutrophication level in the western region was still higher than those in the central and eastern regions. The relief of eutrophication was mainly attributed to the decrease in lake-inlet pollution from Nanfei River, Shiwuli-Tangxi River, and Paihe River. The increasing lake-inlet phosphorus pollution from Zhaohe River (in the central region), Shuangqiao River and Zhegao River (in the eastern region) directly contributed to the worsening trend of water quality in the two regions. In addition, with the increasing of total phosphorus level in the eastern region, the dominant bloom-forming cyanobacterial species in the region had shifted from Dolichospermum to Microcystis in summer, which might be one of the reasons why cyanobacterial blooms area in Lake Chaohu increased abnormally in 2018. Therefore, the pollution control of Lake Chaohu Basin should continue to strengthen the control in the western part of the basin, while increasing the attention and investment in the central and eastern part of the basin.