We used neutron radiography (NR), a non-invasive and in situ technique, to study living plant roots in soil. Plant roots have a larger water content than their unsaturated surrounding media. As water strongly attenuates a neutron-beam, NR can identify root structures in detail. We investigated the use of NR to visualize the root growth of lupin in quartz sand and in a loamy sand field soil. Further experiments elucidated the root growth of lupin in the loamy sand heterogeneously contaminated with 10 and 20 mg kg−1 boron (B) and 100 mg kg−1 zinc (Zn). We obtained high-quality images of root growth dynamics in both media with a resolution range of 110–270 μm. The images with quartz sand revealed fine structures such as proteoid roots that are difficult to locate in situ by other methods without destruction of the soil. Though quartz sand provided excellent visibility of roots, it proved to be a poor medium for growing plants, probably because of its bulk density (1.8 Mg m−3). The images with field soil showed normal root growth with slightly less contrast than the quartz sand. The poorer contrast was due to the greater neutron interaction with soil water and soil organic matter. In the heterogeneously contaminated soil, root growth was significantly reduced in the contaminated part of the soil in all B and Zn treatments. This study shows that NR has potential as a non-invasive method to investigate root growth over time as well as the response of roots to various abiotic stress factors.