n rice, silicon can mitigate abiotic and biotic stresses. We therefore investigated the effect of Si on key root traits related to soil flooding and salinity tolerance with emphasis on the outer apoplastic barrier and cortical aerenchyma. We tested the hypothesis that Si application alters the phenotypic response of these root traits by growing rice in nutrient solutions without or with Si, designed to mimic drained or flooded soils. We measured the barrier strength through resistance to O2 and water of the outer parts of adventitious roots along with cortical aerenchyma and other root structural traits. We found that Si delayed the barrier formation and caused lower amounts of inducible cortical aerenchyma. The delay in barrier formation resulted in higher xylem loading of Na+ and Cl-, i.e., the sap flux of both ions was significantly higher for plants with access to Si. The increased ion fluxes correlated with lower lignin and suberin deposition in the outer part of the root. Consequently, we do not recommend using Si application to alleviate combined stress of salinity and soil flooding in rice, since the barrier was more permeable to O2, and the aerenchyma formation was less pronounced in roots with Si.