Rice (Oryza sativa L.) roots play important role in the absorption of water, nutrients, and also in stress tolerance such as desiccation, salt and drought stress. The root’s anatomical and histological features showed large xylem vessels and reduced aerenchyma formation in resistant genotypes under water stress. Correlation of anatomical changes in parenchymatous cortex region, starch accumulation in the cortex, and outer unicellular layer of epiblema was also found in rice var. Nagina 22, the most acclaimed drought-resistant variety in Asia. Additionally, electrophoresis of proteins extracted from the roots after water stress showed putative induction of 4–5 proteins putatively induced in var. Nagina 22. These findings suggest that a complex network of regulatory pathways of large xylem vessels with lesser aerenchyma formation and higher starch content in tolerant rice varieties are required for the maintenance of water potential and energy storage under water stress.