Although the issue has been of much concern and has subsequently been controlled for years, the environmental risk of excess selenium (Se) in farmlands still has not been eliminated in Se-toxicity areas. Different types of farmland utilization can change Se behavior in soil. Thus, located field monitoring and surveys of various farmland soils in and around typical Se-toxicity areas spanning eight years were conducted in the tillage layer and deeper soils. The source of new Se contamination in farmlands was traced along the irrigation and natural waterway. This research indicated that 22 % of paddy fields increased to Se-toxicity in surface soil led by irrigation with high-Se river water. Selenate is the dominant Se species in rivers (90 %) originating from geological background areas with high Se. Both soil organic matter (SOM) and amorphous iron content played important roles in the fixation of input Se. Thus, available Se was increased by more than twofold in paddy fields. The release of residual Se and eventual bounding by organic matter is commonly observed, thus suggesting that stable soil Se availability seems sustainable for a long time. This study is the first report in China that shows how new soil Se-toxicity farmland is caused by high-Se water irrigation. This research warns that external attention should be paid to the selection of irrigation water in high-Se geological background areas to avoid new Se contamination.