The Tsengwen Reservoir (TWR) is located at 23°16′N, 120°34′E and is the largest reservoir in Taiwan. During 2009 to 2010, deposition of polychlorinated dibenzo-p-dioxin and dibenzofuran (PCDD/F) in ambient air, water bodies and sediments were measured in the TWR area for this study. The monthly atmospheric PCDD/F deposition in the vicinity of the TWR was found to range from 0.206 to 2.43 pg I-TEQ/m2/day. In addition, the PCDD/F levels (11 to 12 fg I-TEQ/L) in the surface water (water depth: 0.5 m) were found to be uniform and well mixed within the upstream, middle and lower reaches of the TWR. The PCDD/F input flux into the reservoir was investigated together with the PCDD/F concentrations at 1–2 cm intervals in two sediment cores collected at the TWR. The year dating within the sediment cores at different depths was estimated from the sedimentation rate (> 17 cm/y) and calculated by 210Pb analysis. The PCDD/F content at different depth within the sediment cores ranged from 0.136 ng I-TEQ/kg d. w. to 0.413 ng I-TEQ/kg d. w. Before the Morakot Typhoon event (June, 2009), the PCDD/F content of the surface sediments ranged from 0.091 to 0.187 ng I-TEQ/kg d. w. as measured at the upstream, middle and lower reaches of the TWR. Interestingly, the PCDD/F content (0.132 to 0.222 ng I-TEQ/kg d. w.) of surface sediments increased somewhat after typhoon event (January, 2010). The PCDD/F input contributed by the enhanced catchment erosion significantly increased to 99% during intensive typhoon periods.