Construction of casade dams in Heihe River had a certain influence on the river water quality. We divided the water into upstream and downstream reaches of dam and natural reaches. To explore the impact of casade dams on the water quality, multivariate statistical methods were used to analyze the spatio-temporal characteristics of water quality based on 24 different sampling sites from december 2017 to august 2018. The results showed that the main impact factors on water quality in Heihe River were water temperature (WT), pH, dissolved oxygen (DO), electrical conductivity (EC), total nitrogen (TN), total phosphorus (TP) and biochemical oxygen demand (BOD₅). WT, EC, BOD₅, chemical oxygen demand (COD_Mn) and TN varied signnificantly on the spatial scales. The water quality of the upstream reaches of dam were greatly affected by BOD₅ and COD_Mn, while WT, EC and TN were the key drivers for the natural reaches and less environmental influence on the downstream water quality. In temporal terms, WT, EC, BOD₅ and ammonia nitrogen excerted the greatest effects on the water quality, with most of the water quality factors changed obviously in non flood seasons. Factors such as temperature, rainfall, hydrological conditions and the joint operation mode of cascade reservoirs were the main factors affecting the seasonality of water quality in the region. The spatial differences were mainly influenced by the exogenous pollutants discharging in Qilian and Zhangye areas, and the influence of sediment retention and accumulation on the environment of dam construction due to the change of hydrodynamic conditions. The results show that exogenous pollution sources were still the main factors, followed by the cascade dam construction as the indirect factors, for the water quality deterioration. Therefore, controlling the exogenous pollution sources caused by human activities in the region, and implementing a reasonable reservoir operation mode according to the seasonal variation of pollutants were the key to improve the river water quality along with the cascade hydropower development.