Breeding for stress adaptive traits without compromising yield and quality remains challenging. Traditional approaches have focused on identifying ‘silver bullet’ large effect genes, often found in related species and progenitor species of bread wheat. These are then introgressed into elite germplasm but often bring significant penalties for yield and quality. To study abiotic stress traits, including salinity stress, we combined high-throughput precision phenotyping, highresolution genotyping (~9 million SNP) and a purpose built (specially constructed) core diversity panel of 618 spring wheat accessions. We developed a haplotype based GWAS approach to dissect complex trait genetics with resolution at the candidate gene level. For salinity stress, we identified several high-confidence QTL, some known but many novel and which contain genes known in other species to be involved in salinity stress response pathways. Our approach to quantitative trait mapping reveals a new way to breed abiotic stress tolerance in wheat with reduced risk for off target penalties caused by linkage drag. When combined with genomic prediction and speed breeding, new abiotic stress varieties can be rapidly developed. Our results demonstrate the power and resolution attainable from combining the latest precision phenotyping methods, high-resolution genomics and genome-wide haplotype-based analysis in dissecting the genetics of what have been largely intractable complex traits.