The objectives of the present work were to study isotope ratios and the inventory of plutonium and uranium isotope compositions in sediments from Lake Obuchi, which is in the vicinity of several nuclear fuel facilities in Rokkasho, Japan. Pu and its isotopes were determined using sector-field ICP-MS and U and its isotopes were determined with ICP-QMS after separation and purification with a combination of ion-exchange and extraction chromatography. The observed ²⁴⁰Pu/²³⁹Pu atom ratio (0.186 ± 0.016) was similar to that of global fallout, indicating that the possible early tropospheric fallout Pu did not deliver Pu from the Pacific Proving Ground to areas above 40°N. The previously reported higher Pu inventory in the deep water area of Lake Obuchi could be attributed to the lateral transportation of Pu deposited in the shallow area which resulted from the migration of deposited global fallout Pu from the land into the lake by river runoff and from the Pacific Ocean by tide movement and sea water scavenging, as well as from direct soil input by winds. The ²³⁵U/²³⁸U atom ratios ranged from 0.00723 to 0.00732, indicating the natural origin of U in the sediments. The average ²³⁴U/²³⁸U activity ratio of 1.11 in a sediment core indicated a significant sea water U contribution. No evidence was found for the release of U containing wastes from the nearby nuclear facilities. These results will serve as a reference baseline on the levels of Pu and U in the studied site so that any further contamination from the spent nuclear fuel reprocessing plants, the radioactive waste disposal and storage facilities, and the uranium enrichment plant can be identified, and the impact of future release can be rapidly assessed.