We evaluated the in vivo fate and physiological behavior of quantum dots (QDs) in Caenorhabditis elegans by GFP transfection, fluorescent imaging, synchrotron radiation based elemental imaging, and speciation techniques. The in situ metabolism and degradation of QDs in the alimentary system and long-term toxicity on reproduction are fully assessed. This work highlights the utility of the C. elegans model as a multiflexible platform to allow noninvasively imaging and monitoring in vivo consequences of engineered nanomaterials.