Antibiotic pollutions in the aquatic environment have attracted widespread attention due to their ubiquitous distribution and antibacterial properties. The occurrence, distribution, and ecological risk assessment of 17 common antibiotics in this study were preformed in a vital drinking water source represented as a river-reservoir system in South China. In general, 15 antibiotics were detected at least once in the watershed, with the total concentrations of antibiotics in the water samples ranging from 193.6 to 863.3 ng/L and 115.1 to 278.2 µg/kg in the sediment samples. For the water samples, higher rain runoff may contribute to the levels of total concentration in the river system, while perennial anthropic activity associated with the usage pattern of antibiotics may be an important factor determining similar sources and release mechanisms of antibiotics in the riparian environment. Meanwhile, the reservoir system could act as a stable reactor to influence the level and composition of antibiotics exported from the river system. For the sediment samples, hydrological factor in the reservoir may influence the antibiotic distributions along with seasonal variation. Ecological risk assessment revealed that tetracycline and ciprofloxacin could pose high risks in the aquatic environment. Taken together, further investigations should be performed to elaborate the environmental behaviors of antibiotics in the river-reservoir system, especially in drinking water sources.