Freshwater aquaculture serves as a significant focal point for antibiotic contamination, yet understanding antibiotic distribution across different aquaculture models and stages remains limited. This study evaluated antibiotic pollution in three distinct freshwater aquaculture models: rice-crayfish coculture, fish aquaculture, and crab-crayfish aquaculture, during various aquaculture stages. Of the 33 target antibiotics, 16 antibiotics were detected, with the total concentrations ranging from 111.81 ng/L to 15,949.05 ng/L in water and 10.11 ng/g to 8986.30 ng/g in sediment. Among these antibiotics, erythromycin and lomefloxacin are prohibited for use in Chinese aquaculture. Dominant antibiotics in water included lincomycin, enrofloxacin, and enoxacin, whereas in sediment, oxytetracycline and erythromycin were predominant. Notably, lincomycin emerged as a dominant antibiotic in aquaculture for the first time. The concentrations of these dominant antibiotics were high compared to other aquaculture settings and exhibited elevated ecological risk. Critical periods for antibiotic contamination in water and sediment were found to be incongruent, occurring during the rainy season in July for water and the dry season in October for sediment. Notably, the rice-crayfish coculture model exerts a good effect in reducing antibiotic pollution. Overall, these findings offer valuable evidence for the healthful and sustainable advancement of aquaculture. Display omitted •Antibiotics in various aquaculture models and stages were investigated.•Main antibiotics in water were LIN, ENR, and ENO, and in sediment were OTC and ERY.•High concentrations of antibiotics occurred in water in July but in sediment in October.•Rice-crayfish coculture is an eco-friendly model for reducing antibiotic pollution.