A dated sediment core collected from Tokyo Bay, Japan, was used to assess the historical inputs of polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs), and coplanar polychlorinated biphenyls (Co-PCBs) from multiple sources. The levels, patterns, and profiles of these compounds in the core were congener-specifically investigated, and the results show that the PCDD and PCDF (PCDD/F) and the Co-PCB inputs increased abruptly from the late 1950s and peaked during the period 1967 to 1972. From 1972 to 1981, the inputs decreased continuously and then generally leveled off. Using principal component analysis, two herbicides widely used in the past, pentachlorophenol (PCP) and chloronitrofen (CNP), as well as combustion processes were identified as the major dioxin sources in Tokyo Bay. The PCB formulations and combustion processes were estimated to be the major sources of Co-PCBs. Furthermore, multiple regression analysis was performed for dioxin-source apportioning, and it was found that the herbicides PCP and CNP have mainly contributed to the PCDD/F burdens since the late 1950s. This study suggests that herbicide-derived PCDD/Fs remaining in agricultural land will continue to run off and pollute the aquatic environment in Japan for a long time.