Abstract Background Well-developed and functional roots are critical to support plant life and reach high crop yields. Their study however, is hampered by their underground growth and characterizing complex root system architecture (RSA) therefore remains a challenge. In the last few years, several phenotyping methods, including rhizotrons and x-ray computed tomography, have been developed for relatively thick roots. But in the model plant Arabidopsis thaliana , in vitro culture remains the easiest and preferred method to study root development, which technically limits the analyses to young seedlings. Results We present here an innovative design of hydroponic rhizotrons (rhizoponics) adapted to Arabidopsis thaliana . The setup allows to simultaneously characterize the RSA and shoot development from seedling to adult stages, i.e. from seed to seed. This system offers the advantages of hydroponics such as control of root environment and easy access to the roots for measurements or sampling. Being completely movable and low cost, it can be used in controlled cabinets. We chose the case of cadmium treatment to illustrate potential applications, from cell to organ levels. Conclusions Rhizoponics makes possible, on the same plants of Arabidopsis , RSA measurements, root sampling and characterization of aerial development up to adult size. It therefore provides a valuable tool for addressing fundamental questions in whole plant physiology.