Antibiotics in the aquatic environment are of great concern as novel contaminants. In this study, we investigated the occurrence, distribution, potential sources, and risk assessment of antibiotics in an interconnected river–wetland–lake system. Thirty-three target antibiotics, including sulfonamides (SAs), macrolides (MLs), fluoroquinolones (FQs), tetracyclines (TCs), and chloramphenicol (CLs) belong to five common groups of antibiotics, were tested from water samples collected in the Panlong River, Xinghai Wetland, and Lake Dian (or Dianchi). Mass spectrophotometry was used to detect the target antibiotics, and the water quality parameters were measured in situ. We found four antibiotics, lincomycin (LIN), trimethoprim (TMP), sulfamethoxazole (SMX), and ofloxacin (OFL), with relatively low concentrations at the ng/L level, and detection rates among sample sites ranged from 42.3% to 76.9%, with maximum concentrations of 0.71 ng/L~5.53 ng/L. TMP was not detected in the Panlong River but appeared in the wetlands and Lake Dian. Midstream urban areas of the Panlong River showed the highest pollution among sites. Antibiotic concentrations were positively correlated with total nitrogen (TN) (p < 0.05) and showed some negative correlation with pH, salinity, and DO. According to the risk assessment, antibiotics in water do not pose a threat to human health and aquatic ecosystems, but a potentially harmful combined effect cannot be excluded. Our research offers a geographical summary of the distribution of antibiotics in urban river, wetland, and lake ecosystems in the plateau (PWL), which is important for predicting the distribution characteristics of antibiotics in the plateau water environment and establishing a standardized antibiotic monitoring and management system for the government.