Antibiotics play an essential role in the aquaculture industry, but their overuse and weak degradability inevitably lead to light to severe residues in natural and aquaculture environments. Most studies were interested in the occurrence, distribution, and ecological risks of a limited number of antibiotics in natural environments (rivers, lakes, and coastal regions) with a minor focus on antibiotic presence in either water, sediments, or organisms in aquaculture environments located in specific regions. In this study, we conducted a comprehensive investigation into the occurrence and distribution of up to 32 antibiotics [including 15 quinolones (QNs) and 17 sulfonamides (SAs)] in organisms and their corresponding environmental matrices from 26 freshwater aquaculture ponds in Northeast Zhejiang, China. A total of 13, 9, 7, and 7 antibiotics were detected in pond water, sediments, feeds, and aquaculture organisms, respectively, with concentration ranges of 0.6–92.2 ng/L, 0.4–1169.3 ng/g dw, <LOD–17.5 ng/g dw, and < LOD–234.3 ng/g ww, respectively, where enrofloxacin (ENR) was the main component in different matrix samples, with a proportion range of 51 %–88 %. There were differences in the predominant antibiotic and concentration abundance among fishponds, shrimp ponds, crab ponds, and turtle ponds. Feed was likely one of the most essential source of antibiotics in freshwater aquaculture ponds. The risk quotient (RQ) results revealed that ciprofloxacin (CIP) and ENR showed high risks to algae in water at the maximum measured concentrations and norfloxacin (NOR), CIP, ENR, and ofloxacin (OFL) exhibited high risks in sediments. However, the joint probability curve (JPC) showed acceptable risk in water. On the basis of the calculated hazard quotients (HQ < 1), the risk of human antibiotic ingestion through aquaculture organisms was acceptable. These results suggest that the rational control of antibiotic use is necessary for human health and ecological security.