The biochemical responses of two tomato cultivars to water logging and drought stress were investigated under glasshouse conditions. We investigated the accumulation of reactive oxygen species, evidence of oxidative stress and activation of the antioxidant defence system (enzymatic antioxidants and non-enzymatic antioxidants) in leaves and roots, after 14 days of exposure to water stress. There were significant intraspecific differences in many stress responses, with lower levels of oxidative damage (hydrogen peroxide accumulation, damage to lipids, proteins and DNA) in the cultivar 'Scoresby Dwarf' under both types of water stress. Waterlogging induced hypoxia as measured by increasing ADH activity in the roots of all plants. Total carotenoid content was reduced in the pericarp of fruits of the cultivar 'Best Boy Bush' grown under water deficit and waterlogging, but not in the pericarp of 'Scoresby Dwarf' fruits. Compared to the stress-tolerant 'Scoresby Dwarf', 'Best Boy Bush' had lower activity of enzymatic antioxidants and lower production of non-enzymatic antioxidants under water stress. In conclusion, the results of this study provide strong proof of distinctive oxidative stress response patterns under the two water stress extremes with clear evidence for intraspecific differences in these responses. The findings from this study improve the understanding of biochemical changes in plants experiencing oxidative stress and can be used for the selection and development of stress tolerant tomato cultivars.