Rice is an important source of selenium (Se) exposure; however, the transformation and translocation of Se in the soil-rice system remain poorly understood. Here, we investigated the speciation of Se in Se-rich soils from Enshi, Central China and assessed which Se species is bioavailable for rice grown in Enshi. Extremely high Se concentrations (0.85 to 11.46 mg/kg) were observed in the soils. The soil Se fractions, which include water-soluble Se (0.2 to 3.4%), ligand-exchangeable Se (4.5 to 15.0%), organically bound Se (57.8 to 80.0%) and residual Se (6.1 to 32.9%), are largely controlled by soil organic matter (SOM) levels. Decomposition of SOM promotes the transformation of organically bound Se to water-soluble Se and ligand-exchangeable Se, thereby increasing the bioavailability of Se. The bioaccumulation factors (BAFs) of Se decrease in the following order: roots (0.84 ± 0.30) > bran (0.33 ± 0.17) > leaves (0.18 ± 0.09) > polished rice (0.14 ± 0.07) > stems (0.12 ± 0.07) > husks (0.11 ± 0.07). Selenium levels in rice plants are affected by multiple soil Se fractions in the soil. Water-soluble, ligand-exchangeable and organically bound Se fractions are the major sources of Se in rice tissues.