This study presents the data concerning the intensity of lipid peroxidation in seedlings of Arabidopsis thaliana, which were grown under the prolonged water stress on the agarized sterile medium. Growth parameters, such as length of the main root and fresh matter were measured. The seedlings of A. thaliana subjected to water deficit exhibited a decrease in the growth of the main root and fresh weight in comparison to the control plants. Since peroxidation processes due to the concentration of malonic dialdehyde and the level of chemiluminescence of plant homogenate decreased at the end of the experiment, it was concluded that plants were able to adapt to water stress conditions.