Most important traits in wheat are complex, quantitatively inherited, and controlled by many minor effect genes. This poses a significant challenge to characterize these traits. Linkage and linkage disequilibrium (LD) mapping approaches have limitations that a multi-parent population approach such as nested association mapping (NAM) can overcome to unlock the genetic basis of complex traits. We established a bread wheat NAM population that takes into consideration genetic diversity and agronomically important traits. The NAM uses a common reference line “Stettler”, a high yielding modern Canadian cultivar, in crosses with donor founder lines consisting of 25 synthetic hexaploid wheat (SHW) lines that were developed by CIMMYT and 25 historical and elite Canadian cultivars. The CanNAM 50 sub-populations consists of 5,102 lines including parents. Data from re-sequencing of the NAM population founder lines to a high depth using an exome capture approach was integrated with available public data to establish a large deep re-sequencing dataset for single nucleotide polymorphism (SNP) discovery on a diverse array of wheat accessions. Fifty lines from each subpopulation to a total of 2,500 were evaluated for flowering time, height, spike related traits, leaf rust and Fusarium head blight (FHB) in the 2018 field season. From the re-sequencing dataset we identified 3.1 million SNPs, with an almost equal number of variants across the A, B and D genomes (averaging approximately 1 variant every 100 bp). Population genetic analysis showed genomic changes in Canadian wheat germplasm occurred over time. Diversity analysis revealed that there is a clear separation between Canadian wheat lines and lines from other countries and we observed a dramatic reduction of diversity in Canadian wheat from c.1930 (around the release of Thatcher). The nucleotide diversity (pi; π) was elevated in the D genome of the synthetic hexaploid founders. A negative Tajima's D value indicated an intensively directional selection on Canadian wheat. Haplotype blocks were identified by linkage disequilibrium (LD) analysis with the largest LD block observed on chromosome 7A. Segregation of evaluated traits followed normal distributions across the NAM population confirming broad variation was captured. More applications for wheat genetic, genomic and evolutionary research exist for this unique resource.