Bread wheat (Triticum aestivum L.) is one of the most important cereal crops for food security. Of all the stresses that curtail wheat productivity, drought has the most detrimental effects. Especially terminal drought stress i.e. at the time of flowering imposes a big challenge to sustain grain production. In the current study, 339 pre-breeding lines derived from three-way crosses of exotics x elite lines were evaluated in the irrigated and drought stress environments at Obregon, Mexico for the year 2016 and 2018. Drought significantly reduced yield (Y), spike length (SL), number of grains per spikes (NGS) and thousand kernel weight (TKW) by 46.4, 19.2, 23.5 and 25.9%, respectively in comparison to irrigated conditions. Kernel abortion (KA), highly correlated with Y, increased significantly (11.6%) under drought stress environment. Population structure analysis in this panel revealed three sub-populations and a genome wide linkage disequilibrium (LD) decay was at 2.5 cM. Single marker and haplotypes-based genome wide association study (GWAS) revealed significant associations on three chromosomes; 4A (HB10.7), 2D (HB6.10) and 3B (HB8.12) with Y, SL and TKW, respectively. Likewise, associations on chromosomes 6B (HB17.1) and 3A (HB7.11) were identified for NGS and on 3A (HB7.12) for KA. Five traits i.e. normalized difference vegetation index (NDVI), canopy temperature depression (CTD) days to heading (DTH), NGS, KA were associated at chromosome 3A both under irrigated and drought conditions however, different haplotypes were estimated. Twenty-six SNPs were part of 10 haplotype blocks associated with Y, SL, TKW, NGS and KA. In silico analysis of the associated SNPs/haplotypes showed hits with candidate genes known to confer abiotic stress resistance in model species and crops. Potential candidate genes include those coding for sulfite exporter TauE/SafE family in Arabidopsis thaliana, TBC domain containing protein in Oryza sativa subsp. Japonica and heat shock proteins in Aegilops tauschii subsp. tauschii were revealed. The SNPs linked to the promising genes identified in the study can be used for marker-assisted selection.