Quantifications of root system architecture and growth dynamics became essential in sustainable agriculture, bio-engineering and underground ecology in general. Assessing of root architectural parameters is still challenging also owing to different methodological challenges and high-cost facilities required. The objective of this study was to design and examine a performance of a simple experimgal set-up for monitoring and analyses of root system architecture. The proposed system was examined with two cover crops – white mustard and sweet clover – grown in sand filled pots under controlled climate conditions for several weeks. Root systems of each crop were harvested in regular intervals of 2 to 3 weeks in 3 to 4 replicates. After careful washing, the intact root systems were photo captured in water filled cylinder in their quasi-natural position over entire rotation and then scanned using a flatbed professional scanner. The gained images (photos and scans) were analysed with AutoCAD and WinRhizo software for measuring of diverse root architectural parameters for modelling. The results showed that the selected experimental and methodical approaches were appropriate for monitoring and delivering data of good quality. Both, digital camera and scanner were regarded as essential complementary imaging tools for correct assessment of the root system architecture. To maximise the accuracy of the measurements, recommendation for improving the system were provided. Extracted root data are intended for parametrisation of root architectural models, but they also support researcher and experts in their efforts to improve crop uptake efficiency in sustainable agriculture and for bio-engineering purposes.