As antibacterial active ingredients, biocides are widely used in medicines, personal care products, food, agriculture, and other sectors. Large amounts of biocides enter aquatic environments directly or via effluents of wastewater treatment plants (WWTPs), which might pose negative effects on ecological environments and human health. In this study, the occurrences, distributions, and ecological risks of 13 biocides in the sediments of 61 lakes in the middle and lower reaches of the Chnagjiang River were investigated. Eleven biocides, including 5 fungicides, 1 antifouling agent, 3 parabens, and 2 disinfectants, were detected in these lake sediments, with total concentration levels up to 103 ng/g dry weight (dw). The detection frequencies of carbendazim and methylparaben were both greater than 50%, which were 100% and 96.2%, respectively. The mean concentrations of carbendazim and methylparaben were (1.79±2.76) and (11.4±8.19) ng/g, respectively, while the mean concentrations of other compounds were lower than 1.0 ng/g. Compared with other rivers and lakes abroad, the pollution of biocides in area of this study would be ranked at low-medium levels, with the mean value of total biocide concentration of (16.7±14.5) ng/g. Domestic sewage might be the main source for fluconazole, clotrimazole, triclosan and triclocarban, while carbendazim and thiabendazole might come from non-point sources. The distributions of parabens in the lake sediments were significantly related with total organic carbon of the sediments. The ecological risk assessment of biocides in the lake sediments were performed by using risk quotient. Carbendazim, methylparaben and triclocarban showed high ecological risks at some sampling sites. To reduce the adverse effects of biocides on aquatic organisms and human health, it is necessary to take proper measures to control the pollution of biocides in the lake environments, especially at the source area of drinking water.