Water stress accelerates the generation of reactive oxygen species, which trigger a cascade of antioxidative defence mechanisms comprising enzymatic and nonenzymatic antioxidants. The aim of this study was to investigate the oxidative damage and the antioxidative defence systems in seedlings of the water stress-tolerant (B71) and the sensitive (B59) inbred lines of sunflower (Helianthus annuus L.) in response to water stress and rewatering. In addition, we characterised the transcriptomic profile associated with enzymatic antioxidative defence. An elevated electrolyte leakage in B59 indicated increased plasmatic membrane permeability, which correlated with greater sensitivity to water stress. In response to water stress, both lines showed an increase in malondialdehyde and H2O2 content but these increases were more noticeable in the sensitive line. In both lines, an increase in enzymatic activity (e.g. peroxidase and ascorbate peroxidase) was not sufficient to overcome the H2O2 accumulation triggered by water stress. Upon water stress, the overall expression level of genes associated with the enzymatic antioxidant system increased in B71 and decreased in B59, which showed downregulated levels of most genes in the shoots. The general profile of phenolic compounds was clearly different between organs and between inbred lines. The B59 line activated nonenzymatic antioxidant responses to counteract the oxidative stress caused by water stress. The tolerance of B71 to water stress could be associated with compensatory antioxidant mechanisms based on the expression of genes encoding enzyme components of the ascorbate-glutathione and redoxin cycles, which contributed to explaining, at least partly, the response of this line.