Crop yields are reduced by 70–80% due to a water stress situation specifically during the reproductive stage and are not able to fulfil the needs of food requirement in developed and developing countries of the world. Earlier work was mainly focused on the use of morphological or physiological and molecular aspects for improved stress tolerance. Efforts are being made to overcome this problem with the help of today’s sophisticated and advanced technology through genomics, proteomics and metabolomics. The presented model summarizes our work in the last five years to mine anatomical parameters as a novel approach to further improving introgression or exploitation of stress adaptive traits. We have focused on some key anatomical traits playing a substantial role in water stress tolerance. This new conceptual model encompasses increased palisade mesophyll height, higher leaf strength index (LSI), higher number of conducting tissues with increased diameter in leaf, stem and root and controlled transpiration rate due to a lower number of stomata per unit leaf area along with the increased guard cell size. Different plants viz. Lycopersicon esculentum, Capsicum annuum, and Calotropis gigantea were screened by developing polyploids to validate this model approach. Genotypes of Vitis vinifera and Solanum melongena were also screened. Wild relatives like Lycopersicon esculentum var. cerasiforme and Solanum khasianum were evaluated for comparison. These observations were further correlated with various stress adaptation traits like yield under stress, in vitro screening, chlorophyll content, transpiration heating and cooling, molecular markers etc. A new scoring method is proposed which will be helpful to screen a large set of germplasms on a preliminary basis to discriminate genotypes for drought tolerance. There is an urgent need to study the genetics of these stress adaptive traits using high throughput molecular markers to make them more useful for a higher magnitude of genetic gain.