Brassica napus L. plants are sensitive to water stress throughout their life cycle from seed germination to seed setting. This study aims to identify quantitative trait loci (QTL) linked to B. napus tolerance to water stress mimicked by application of 10 % polyethylene glycol-6000 (PEG-6000). Two doubled haploid populations (1901 and 1904), each consisting of 150 genotypes, were used for this research. Plants at the two-true leaf stage of development were grown in the absence (control) or presence (water stress) of PEG-6000 under controlled environmental conditions for 48 h, and the drought stress index (DSI) was calculated for the fresh weight and dry weight of whole plant, root, and shoot of each genotype. The 300 genotypes along with their parents were genotyped using the Brassica Infinium 90K SNP BeadChip Array. Inclusive Composite Interval Mapping was used to identify and confirm QTL. Eighteen QTL associated with water stress tolerance were identified across six chromosomes (A2, A3, A4, A9, C3, and C7). Collectively, 2,154 putative candidate genes for drought stress tolerance in B. napus were identified for all the identified QTL. Among them, 213 genes were chosen as directly associated with drought stress tolerance based on nine functional annotations. These results can be incorporated into future breeding initiatives to select plant material with the ability to effectively cope with water stress.