Silicon (Si) reduces arsenic (As) levels in rice shoot and grain. However, the underlying mechanisms remain unclear. In this study, we examined the effect of Si application to three rice paddy soils on the dynamics of Si, iron (Fe), phosphorus (P), and As in the soil solution, As accumulation in rice straw, flag leaf, husk, brown rice, and polished rice, and on As speciation in polished rice. Silicon application to soil increased the concentrations of Si, Fe, As, and P in the soil solution, while the redox potential was unaffected. Arsenic concentrations of straw, flag leaf, and husk were reduced by half by Si application, while As concentrations of brown and polished rice were decreased by 22%. The main As species in polished rice was arsenite, As(III), with a fraction of 70%, followed by dimethylarsinic acid (DMA) and arsenate, As(V), with 24% and 6%, respectively. Silicon application to the soil did not affect DMA or As(V) concentration of polished rice, while the As(III) concentration was reduced by 33%. These results confirm that Si reduces As(III) uptake and translocation into the shoot. Furthermore, data indicate that decrease of As concentration of polished rice is due to decreased As(III) transport into grain. Possible underlying mechanisms are discussed.