Abiotic stresses are major constraints to wheat productivity in many parts of the world. Tolerance to abiotic stresses can be achieved indirectly by selection for morpho-physiological traits. Physiological trait based breeding has been associated with improved performance under stress; and hence can combat and adapt wheat to drought and heat stress. Therefore, in the present study, phenotyping was carried out for agro-physiological traits in 52 diverse wheat germplasm lines under timely sown, rainfed and late sown environments for two years. Mean yield of the genotypes over the six environments were positively correlated with NDVI, days to maturity and negatively correlated with canopy temperature. The phenotypic data validated marker-trait associations of a number of meta-QTLs identified earlier for different physiological and agronomic traits. Six and seven meta-QTL genomic regions were found to be consistent in their expression for two years under rainfed/restricted irrigation and late sown environments, respectively. Expression analysis of the underlying candidate gene AK248593.1 in meta-QTL26 region revealed two folds higher expression in the NILs carrying the co-localized SSR markers. The linked markers of the thirteen meta-QTL regions associated with different traits can be used for effective transfer of the QTLs through marker assisted selection in wheat breeding programmes.