The content and congener profiles of 17 PCDD/Fs were measured in an aquatic system in central Taiwan that included both aquatic animals and sediment. The total averaged mass content of PCDD/Fs was 0.432, 0.671, 0.244 and 0.727 pg g–1, and the corresponding total PCDD/Fs-WHO2005-TEQ were 0.070, 0.015, 0.024 and 0.018 pg WHO2005-TEQ g–1 in O. mossambica, M. meretrix, L. calcarifer and O. gigas, respectively. The total PCDD/Fs in the sediment in the coastal area (72.63 ng kg–1) was much higher than that in the fishponds (29.53 ng kg–1), but the corresponding WHO2005-TEQ values in the coastal area (0.545 ng WHO2005-TEQ kg–1) were lower than those in the fishponds (0.655 ng WHO2005-TEQ kg–1). The mass PCDD/F congener profiles of the aquatic animals and sediment samples in the fishponds and coastal area were dominated by more highly chlorinated PCDD/F congeners such as OCDD and OCDF, while the WHO2005-TEQ PCDD/F congener profiles were dominated by the less-chlorinated PCDD/F congeners such as 1,2,3,7,8-PeCDD and 2,3,4,7,8-PeCDF. Over a time periods ranging from 30 and 60 years, the modeled PCDD/F contents in the sediment ranged between 9.27 and 18.53 ng WHO2005-TEQ kg–1 in scenario A, and the PCDD/F contents ranged from 6.18–12.36 ng WHO2005-TEQ kg–1 in scenario B. Compared with the observed average values of sediment in this study, the ratios of the modeled and observed values ranged from 9.4–34.0.