Paddy soils and sediments from the Yoneshirogawa, Omonogawa, and Koyoshigawa River Basins in Akita were analyzed for polychlorinated dibenzo-p-dioxins (PCDDs) and dibenzofurans (PCDFs). The levels and compositions in those samples including soils from non-agricultural areas (non-agricultural soils) were investigated using isomer-specific analysis to determine characteristic sources. The PCDD/PCDF compositions in the samples were compared with respect to possible sources. The PCDD/PCDF concentrations in paddy soils were much higher than those in the non-agricultural soils and much higher than those found in other parts of Japan. Although PCDD/PCDFs were ubiquitous in sediments from river sources to mouths of the respective river basins, those concentrations were much lower than those from paddy soils and non-agricultural soils, and from other parts of Japan. Comparison of PCDD/PCDF homologues and isomer compositions for samples indicated that compositions of paddy soils and sediments, except for those from river sources, had similar characteristics to PCDD/PCDFs originating from impurities in herbicides, 2,4,6-trichlorophenyl 4-nitrophenyl ether (CNP) and pentachlorophenol (PCP), and that compositions of river-source sediments and non-agricultural soils resembled those of atmospheric depositions. Results of statistical analyses suggest that PCDD/PCDF contamination of paddy soils and sediments is attributable mainly to three sources: CNP, PCP, and atmospheric deposition. Results of this study also demonstrate that CNP and PCP are not only important contaminants of local areas of Japan, but that they exist throughout Akita, in northern Japan. We therefore conclude that PCDD/PCDF pollution caused by those compounds has a widespread influence on paddy soils and river sediments in Japan.