Lack of understanding of dioxins mass loading into the aquatic environment motivated the quantitative investigation of dioxins runoff from paddy fields during one entire irrigation period in the Minakuchi region, Japan. Combination use of the chemically activated luciferase gene expression (CALUX) bioassay together with high resolution gas chromatography and high resolution mass spectrometry (HRGC/HRMS) enabled efficient investigation of dioxins contamination. The result shows that the congener profile in irrigation runoff is quite similar to those in paddy soil samples and that 1,3,6,8-/1,3,7,9-TeCDD and OCDD derived from pesticides (i.e., pentachlorophenol (PCP) and chloronitrophen (CNP)) are predominant congeners in irrigation runoff. Although it is not surprising that dioxins concentration was strongly dependent on the suspended solids (SS) and the particulate organic carbon (POC) concentration, the dioxins toxic equivalency (TEQ) concentration was extremely high in irrigation runoff (max: 16,380 pg/L, corresponding to 12 pg WHO-TEQ/L) due to runoff of highly contaminated paddy soils. The results imply that dioxins concentration in a river must be monitored considering soil contamination level, land use, and soil runoff events. Using experimental data and a theoretical model, the mass loading of dioxins from the paddy fields by irrigation runoff was estimated to be 1.50 x 10(-2)% of total amount of dioxins accumulated in the paddy fields. Given the results of other researches, it is implied the following: 1) large portion of paddy soils released into the river appear to be settled on the riverbed due to small water flux, and, then, washed out and transported by rainfall runoff after irrigation period, 2) rainfall runoff itself also wash out paddy soils directly from paddy fields. Combination use of the CALUX bioassay with HRGC/HRMS is demonstrated as an alternative strategy to assess dioxins contamination in the environment.