A comparative study of the response to waterlogging in a tolerant (Trifolium repens L., white clover cultivar Rivendel) and susceptible (Trifolium pratense L., red clover cultivar Raya) plants was undertaken to reveal the possible link between plant performance and oxidative stress protection mechanisms in leaves. Two weeks of soil waterlogging induced visible leaf damage in the susceptible genotype. In the tolerant one, signs of stress suffering appeared a week later. Waterlogging induced hydrogen peroxide accumulation in both clover species. The content of lipid hydroperoxides markedly increased in the sensitive plants along with stress prolongation, while in the tolerant ones their initial rise was followed by return to control levels. In the leaves of both genotypes ascorbic acid content increased following treatment, accompanied by transient increase in oxidized ascorbate. Superoxide dismutase (SOD) isoforms responded differently to the treatment, CuZn SOD isoforms being inhibited; catalase activity diminished while peroxidase activity increased and a new peroxidase isoform was detected after prolonged waterlogging in both clover species. Results support more pronounced oxidative secondary stress in red clover leaves as a result of waterlogging with progressively increased oxidative membrane injury, protein loss, and peroxidase activity enhancement. White clover presented relative protein stability and earlier and more active ascorbate involvement in the antioxidative protection.