Cyanobacterial blooms can generate various toxic metabolites in freshwater, and pose serious threats to drinking water safety and human health. Although microcystins (MCs) have been detected in many freshwater ecosystems in China, little is known about the other cyanotoxins. An investigation of six eutrophic lakes (i.e. Hulun Lake, Wuliangsuhai Lake, Chaohu Lake, Taihu Lake, Xingyun Lake, and Dianchi Lake) in different geographical locations of China was performed during the summer of 2022 to determine the occurrence of various cyanotoxins (i.e. anatoxin-a (ATX), cylindrospermopsin (CYN), and MCs) in water column and their possible risks, and to evaluate the related environmental factors. MCs levels in sediment of these lakes were also investigated. MCs were the primary cyanotoxins in the water column of investigated lakes. The mean MCs contents in water column of Hulun Lake, Wuliangsuhai Lake, Chaohu Lake, Taihu Lake, Xingyun Lake, and Dianchi Lake were 3.61, 0.13, 3.60, 2.18, 0.57, and 2.56 μg/L, respectively. The total MCs levels in water column exceeded 1 μg/L in some areas of these lakes except Wuliangsuhai Lake. Replete nitrogen and/or phosphorus levels seemed to be related to MCs production. ATX can be detected in these lakes except Xingyun Lake at ng/L levels. CYN can be detected in all lakes at ng/L levels. However, the levels of ATX and CYN appear to be not significantly associated with environmental factors. MCs and CYN can pose a high or moderate risk for humans and aquatic organisms in some areas of these lakes, while ATX can pose a low or no risk for humans and aquatic organisms in most areas of these lakes. MCs can also be detected in sediment of all lakes at ng/g levels. This research emphasizes the necessity for long-term monitoring of different cyanotoxins in eutrophic lakes, and the implementation of nutrient control and management strategies.