Abstract: With the country attaches more attention on the ecological environment and strengthens regulation on environmental protection, changes in the water quality of China's rivers and lakes and the effectiveness of control measures such as pollution control have increasingly become the focus.Through the monitoring data collection from different industries, departments and scientific research units on the Changjiang River main stream and a number of water quality and eutrophication data of typical lakes in the basin, it is found that in the last decade or so, the Changjiang River Basin and even the whole country wide water quality of rivers have improved significantly, but the lake water quality enhancement is less obvious, eutrophication and cyanobacterial blooms have not been significantly improved, and some lakes are even aggravated.The main reasons for this situation include the characteristics of the water body itself and the external drive in two aspects:(1) The water exchange rate in the lake is slower than rivers, so that pollutants and nutrients are more likely to be retained in the lakes.At the same time, nitrogen, phosphorus and other nutrients have deposited at the bottom of lakes for a long time, which are very easy to be released again due to the wind and waves and other disturbances to produce endogenous pollution, thus greatly slowing down or offsetting the recovery of the water quality in the lakes.(2) Under the background of global climate change, the time of cyanobacterial bloom outbreaks is advanced, the duration is prolonged, and the frequency of outbreaks is increased, which further aggravate the intensity of cyanobacterial bloom production in eutrophic lakes.The control of eutrophication and cyanobacterial bloom management in shallow lakes in the middle and lower reaches of Changjiang River would be a long and arduous task.