Molybdenum (Mo) contamination of farmland soils poses health risks due to Mo accumulation in crops like rice. However, the mechanisms regulating soil availability and plant uptake of Mo remain poorly understood. This study investigated Mo uptake by rice plants, focusing on Mo speciation and isotope fractionation in soil and rice plants. Soil Mo species were identified as sorbed Mo(VI) and Fe-Mo(VI) using X-ray absorption spectroscopy (XAS). Soil submergence during rice cultivation led to the reductive dissolution of Fe-associated Mo(VI) while increasing sorbed Mo(VI) and Ca-Mo(VI). Soil Mo release to soil solution was a dynamic process involving continuous dissolution/desorption and re-precipitation/sorption. Mo isotope analysis showed soil solution was consistently enriched in heavier isotopes during rice growth, attributed to re-sorption of released Mo and the uptake of Mo by rice plants. Mo was significantly associated with Fe in rice rhizosphere as sorbed Mo(VI) and Fe-Mo(VI), and around 60 % of Mo accumulated in rice roots was sequestrated by Fe plaque of the roots. The desorption of Mo from Fe hydroxides to soil solution and its subsequent diffusion to the root surface were the key rhizosphere processes regulating root Mo uptake. Once absorbed by roots, Mo was efficiently transported to shoots and then to grains, resulting in heavier isotope fractionation during the translocation within plants. Although Mo translocation to rice grains was relatively limited, human exposure via rice consumption remains a health concern. This study provides insights into the temporal dynamics of Mo speciation in submerged paddy soil and the uptake mechanisms of Mo by rice plants.