In order to assess how environmental factors are affecting the distribution and migration of radioiodine and plutonium that were emitted from the Fukushima Dai-ichi Nuclear Power Plant (FDNPP) accident, we quantified iodine and (239,240)Pu concentration changes in soil samples with different land uses (urban, paddy, deciduous forest and coniferous forest), as well as iodine speciation in surface water and rainwater. Sampling locations were 53-63 km northwest of the FDNPP within a 75-km radius, in close proximity of each other. A ranking of the land uses by their surface soil (<4 cm) stable (127)I concentrations was coniferous forest > deciduous forest > urban > paddy, and (239,240)Pu concentrations ranked as deciduous forest > coniferous forest > paddy ≥ urban. Both were quite distinct from that of (134)Cs and (137)Cs: urban > coniferous forest > deciduous forest > paddy, indicating differences in their sources, deposition phases, and biogeochemical behavior in these soil systems. Although stable (127)I might not have fully equilibrated with Fukushima-derived (129)I, it likely still works as a proxy for the long-term fate of (129)I. Surficial soil (127)I content was well correlated to soil organic matter (SOM) content, regardless of land use type, suggesting that SOM might be an important factor affecting iodine biogeochemistry. Other soil chemical properties, such as Eh and pH, had strong correlations to soil (127)I content, but only within a given land use (e.g., within urban soils). Organic carbon (OC) concentrations and Eh were positively, and pH was negatively correlated to (127)I concentrations in surface water and rain samples. It is also noticeable that (127)I in the wet deposition was concentrated in both the deciduous and coniferous forest throughfall and stemfall water, respectively, comparing to the bulk rainwater. Further, both forest throughfall and stemflow water consisted exclusively of organo-iodine, suggesting all inorganic iodine in the original bulk deposition (∼ 28.6% of total iodine) have been completely converted to organo-iodine. Fukushima-derived (239,240)Pu was detectable at a distance ∼ 61 km away, NW of FDNPP. However, it is confined to the litter layer, even three years after the FDNPP accident-derived emissions. Plutonium-239,240 activities were significantly correlated with soil OC and nitrogen contents, indicating Pu may be associated with nitrogen-containing SOM, similar to what has been observed at other locations in the United States. Together, these finding suggest that natural organic matter (NOM) plays a key role in affecting the fate and transport of I and Pu and may warrant greater consideration for predicting long-term stewardship of contaminated areas and evaluating various remediation options in Japan.