In rainfed agroecosystems, water scarcity reduces the yield of rice by impairing the functionality of roots and reducing water uptake. The study evaluated morphological and anatomical properties of roots of 28 rice varieties that were planted under both irrigated and rainfed conditions in a rainout shelter during the 2020–21 kharif season. Root characteristics 45 days following sowing were measured using mini-rhizotrons and WinRhizo imaging; identified genotypes were subsequently analysed by scanning electron microscopy (SEM) to measure cortical architecture and aerenchyma development. There was a great variation in the genotypes in cumulative root length, surface area, mean diameter and volume. Under rainfed conditions, DT-122 retained longer root length, surface area and volume with preserved cortical cells and aerenchyma structure. Contrary to this, DT-127 was also found to reduce root length and volume, impair cortical cells and generate less aerenchyma. These different reactions suggest two different adaptive patterns: DT-122 use a mixture of anatomical stability and wide soil exploration whereas DT-127 seems to be more adaptable to irrigated areas. Even though aerenchyma promotes aeration and mechanical support of flooded soils, it can impair root functionality during droughts, which is a trade-off in drought tolerance. Combination of morphological and anatomical studies produced a more detailed evaluation of the performance of genotypes in water stress. DT-122 is a potential candidate to upland rice breeding, but multilocation trials to determine the correlation between root characteristics and water extraction depth and grain yield are required to determine its usefulness.