Fish culture in lakes is an important component of aquaculture in some countries, but little is known about its impact on the ecosystem of the impacted lake. In summer 2015, we measured concentrations of 11 heavy metals, including copper (Cu), zinc (Zn), lead (Pb), arsenic (As), and manganese (Mn), in water and sediment from 23 lakes of different aquaculture classifications in the middle reach of the Yangtze River basin, China. These lakes represented the following four lake aquaculture management strategies: fish ranching in lakes classified as receiving low (LOW; used for backup drinking water and irrigation), medium (MEDIUM), or high (HIGH; fish fed commercial feed) stocking rates or as fallow (FALLOW), in which previously ranched HIGH lakes had not been stocked for 2 years. Results showed a positive relationship between most heavy metal concentrations and fish culture intensity. Concentrations of Cu, Zn, and aluminum (Al) in the water column were significantly greater in the HIGH lakes than in the LOW lakes. Heavy metals in the FALLOW lakes did not appear to fully recover from past aquaculture activities. In sediment, the concentration of As in LOW lakes was significantly lower than those in MEDIUM and HIGH lakes, whereas no among‐group significant differences in the other heavy metal concentrations were detected. Metals in sediments of all four lake types were at the low ecological risk level. We speculate that these results may be applied to lakes in other regions globally with similar fish stocking and management strategies.