Due to their unique properties, nanomaterials (NMs) behave peculiarly in biosystems. Regarding plants, the interactions of NMs can be interpreted on a spatial scale: from local interactions in cells to systemic effects on whole plants and on ecosystems. Interpreted on a time scale, the effects of NMs on plants may be immediate or subsequent. At the cellular level, the composition and structure of the cell wall and membranes are modified by NMs, promoting internalization. The effects of NMs on germination and seedling physiology and on the primary and secondary metabolisms in the shoot are realized at organ and organism levels. Nanomaterials interact with the beneficial ecological partners of plants. The effects of NMs on plant growth-promoting rhizobacteria and legume-rhizobia symbiosis can be stimulating or inhibitory, depending on the concentration and type of NM. Nanomaterials exert a negative effect on arbuscular mycorrhiza, and vice versa. Pollinators are exposed to NMs, which may affect plant reproduction. The substances released by the roots influence the availability of NMs in the rhizosphere and components of plant cells trigger internalization, translocation, and transformation of NMs. Understanding of the multilevel and bidirectional relationship between plants and NMs is of great relevance in practice.