Abiotic stresses, especially drought, may seriously affect soybean yield. Due to the complexity of drought tolerance, one of the difficulties in selecting genotypes is the identification of traits contributing to improve stress tolerance. This study carried out soybean phenotyping under water deficit in vegetative and reproductive stages in field conditions at two consecutive crop seasons (2012/13 and 2013/14). The experiment was performed in Londrina, PR, Brazil, with two soybean cultivars with distinct levels of drought tolerance, BR 16 (sensitive) and Embrapa 48 (less sensitive). Water deficit was applied through rainout shelters, moving on rails to cover plots when the rainfall begins and uncover them when it ends. Then, some agronomic and morphological traits were measured. Multivariate statistics through the principal component analysis (PCA) associated with the biplot graph identified traits contributing to greater yield stability under drought. Result showed that water deficit affected soybean yield, mainly in the reproductive stage, in which Embrapa 48 had greater yield stability when compared to BR 16. However, opposite results were obtained for stress induced in the vegetative stage, when Embrapa 48 was more negatively affected than BR16 cultivar. Seed weight influenced yield differences between cultivars. Lighter seeds, but in larger number, constituted an advantage under water deficit. Due to the difficulty in introducing all drought tolerance mechanisms in one genotype, breeding programs need to define selection parameters according to regional drought conditions.