The sensitivity of seed composition to drought was compared among three spring glasshouse-grown rapeseed genotypes by applying water shortage treatments at various stages of development. All traits under study associated with the biochemical composition of the seed were drastically modified in plants subjected to drought during flowering. Water shortage during a restricted period in the early stages of vegetative growth was also important for seed quality. Despite limited fluctuations in total lipid content, changes in fatty acid composition were found, especially in the erucic acid metabolic pathway (i.e., oleic, gadoleic and erucic acids). A slight increase in seed protein concentration was observed after early vegetative and flowering drought treatments. The total sugar content of seeds was not significantly affected by water deprivation. Significant effects of drought stress, depending on its timing, were observed in the accumulation of secondary metabolites (i.e., phenolics and glucosinolates) which are of major importance for rapeseed meal quality. The relevance of the observed effects on seed composition resulting from either immediate or long-term effects of water deprivation depending on its application stage is discussed.