Lakes are regarded as copious antibiotic reservoirs because the antibiotics discharged by human activities mostly end up in lakes and further threaten the aqueous ecosystem. Antibiotic contamination in lakes is mostly attributed to wastewater treatment plant effluents, which change the water quality and pose ecological risks. This study investigated the concentration of 10 selected antibiotics in 17 lakes along the middle and lower reaches of the Yangtze River Basin. The correlation between antibiotics and water quality parameters were analyzed. Seven out of the 10 selected antibiotics were detected in almost all the 17 lakes with the highest concentration at 1139.40 ng/L. Sulfamethoxazole (SMZ) and erythromycin (ERY) had relatively higher concentration compared with other antibiotics. Antibiotic detection frequency was approximately 40%-100% in all 17 lakes. Ofloxacin (OFX) and naproxen (NPX) were negatively correlated (p < 0.05) with redox potential, indicating their oxidation potential in freshwater lakes. OFX showed high or medium short-term risks in some of the lakes and low or insignificant long-term risks in the corresponding lakes, respectively. In contrast, sulfadiazine and SMZ exerted low and medium short-term ecological risks and medium and high long-term risks, respectively. Roxithromycin (ROX) showed low short-term risk in seven of the 17 lakes and medium long-term risk in the corresponding lakes. NPX showed insignificant short-term and long-term risks in almost all the 17 lakes. This study fills the gap on antibiotic ecological risk assessment along the Yangtze River Basin and reveal the importance of SMZ control in the research area.