Soil salinity is a major environmental stress that adversely affects the growth, development, productivity, and quality of crop species, in particular, in arid and semi-arid regions. Identification of chromosomal regions associated with agronomic traits under salinity stress is crucial for improving salinity tolerance in wheat. Genome-wide association study (GWAS) was employed to evaluate 289 elite lines of the Wheat Association Mapping Initiative (WAMI) population under low (LS) and high (HS) salinity conditions using 15,737 SNP markers for seven agronomical traits. The genotypes responded differently to the different environments for all traits, highlighting genetic diversity within the WAMI population in response to salt stress, where the heritability ranged from moderate (37%) to high (88%). GWAS identified 118 and 120 significant marker-trait associations (MTAs) under LS and HS conditions, respectively. Significant association of some markers with more than one phenotypic trait was observed, indicating possible pleiotropic or indirect effects. A high degree of significant linkage disequilibrium (> 52%) was observed among SNPs on different chromosomes, indicating epistatic interaction. The salt stress index (STI) exhibited a positive significant correlation to grain yield per plant (GYP) under both LS and HS conditions (R² = 0.851–0.856). Linear regression analysis between STI and GYP under HS conditions indicated that STI is the best tolerance index for predicting high-yielding genotypes. The results present the WAMI population as a valuable source for improving yield potential for salt tolerance in wheat. Furthermore, our findings emphasize that GWAS is a powerful tool in promoting wheat breeding through accurate identification of molecular markers significantly associated with agronomic traits, which is essential for marker-assisted breeding.