During the last decades, nanotechnology has found application in almost all sciences, particularly in biology, chemistry, physics, mechanics, medicine and pharmacy. The final product of this interdisciplinary branch are nanoparticles, which differ from the original materials due to their improved properties. A special group are metal nanoparticles (MNPs), whose application is particularly popular in agriculture, where they are used in the composition of pesticides and artificial fertilizers, which very often leads to negative, phytotoxic effects on plants and thus on the environment. The interactions of MNPs with plants cause damage at morphological, physiological and genetic levels. Different types of MNPs such as silver nanoparticles (AgNPs) and copper and zinc oxide nanoparticles (CuO-NPs and ZnO-NPs) can damage plant roots, but also subcellular components, i.e. cell organelles and important biological macromolecules such as the DNA molecule, cause changes and disturbances in the photosynthesis process and increase the accumulation of harmful reactive oxygen molecules. The above damages are the result of different properties of MNPs, and their phytotoxicity largely depends on the type and concentration of MNPs used and the plant species.