The present study determines the influence of three ionic liquids (ILs) containing cations with diversified structure on the growth and development of spring barley seedlings and common radish leaves. Increasing amounts of 1-butyl-1-methylpyrrolidinium hexafluorophosphate [Pyrrol][PF6], 1-butyl-1-methylpiperidinium hexafluorophosphate [Piper][PF6], and 1-butyl-4-methylpyridinium hexafluorophosphate [Pyrid][PF6] were added to the soil on which both plants were cultivated. The results of this studies showed that the applied ILs were highly toxic for plants, demonstrated by the inhibition of length of plant shoots and roots, decrease of fresh mass, and increase of dry weight content. Common radish turned out to be the plant with higher resistance to the used ILs. The differences in the cation structure did not influence phytotoxity of ILs for spring barley. Furthermore, all ILs led to a decrease of photosynthetic pigments, which was directly followed by decreased primary production in plants. Oxidative stress in plants occurred due to the presence of ILs in the soil, which was demonstrated by the increase of malondialdehyde (MDA) content, changes in the H2O2 level, and antioxidant enzymes such as superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD). The changes in the chlorophyll contents and the increase of POD activity turned out to be the most significant oxidative stress biomarkers in spring barley and common radish. Both spring barley and radish exposed to ILs accumulated a large amount of fluoride ion.Electronic supplementary materialThe online version of this article (doi:10.1007/s11356-017-9439-x) contains supplementary material, which is available to authorized users.