As nanotechnology rapidly emerges into a new industry - driven by its enormous potential to revolutionize electronics, materials, and medicine - exposure of living species to discharged nanoparticles has become inevitable. Despite the increased effort on elucidating the environmental impact of nanotechnology, literature on higher plants exposure to nanoparticles remains scarce and often contradictory. Here we present our biophysical methodologies for the study of carbon nanoparticle uptake by Allium cepa cells and rice plants. We address the three essential aspects for such studies: identification of carbon nanoparticles in the plant species, quantification of nanotransport and aggregation in the plant compartments, and evaluation of plant responses to nanoparticle exposure on the cellular and organism level. Considering the close connection between plant and mammalian species in ecological systems especially in the food chain, we draw a direct comparison on the uptake of carbon nanoparticles in plant and mammalian cells. In addition to the above studies, we present methods for assessing the effects of quantum dot adsorption on algal photosynthesis.