Nanotechnology permits broad advances in agriculture. However, as it is still at a relatively early stage of development, the potential risks remain unclear. Herein, for the first time, we reveal the following: 1) the impact of multi-walled carbon nanotubes (MWCNTs) on the accumulation/depuration behaviors of contaminants in crop, mustard (Brassica juncea), and 2) the permeability and transportability of MWCNTs in intact mature mustard plants. Using an in vivo sampling technique, the kinetic accumulation/depuration processes of several contaminants in mustard plans exposed to MWCNTs were traced, and an enhancement of contaminant accumulation in living plants was observed. Meanwhile, we observed that the MWCNTs permeated into the roots of intact living plants (three months old) and were then transported to the upper organs under the force of transpiration steam. This study demonstrated that MWCNTs can act as contaminant carriers and be transported to the edible parts of crops.