High-throughput phenotyping has substantially advanced the understanding of shoot-level stress responses; however, progress in root phenotyping remains limited. Traditional root studies are destructive, time-consuming, and unsuitable for dynamic monitoring. Here, we present applications of the PlantScreen™ Root System, an automated, non-invasive platform enabling parallel monitoring of root and shoot growth across multiple plant species. The system allows precise control of rhizobox soil moisture, facilitating either waterlogging or drought treatments, and supports the application of defined nutrient and biostimulant regimes. Within the framework of the BarleyMicroBreed project, root growth dynamics of ten barley genotypes were characterized at early developmental stages under optimized moderate drought conditions. Simultaneous analysis of root and shoot growth complements field-trial evaluations aimed at assessing the contribution of root traits to plant performance, particularly yield stability under drought. Morphological traits of shoots and roots were captured using RGB imaging, while multispectral and near-infrared sensors provided additional insights into physiological properties, including root water content. Automated image segmentation using a sensor-specific pipeline with a pretrained model, followed by trait extraction, enabled efficient quantitative trait analysis. The results revealed distinct, genotype-dependent responses to drought, reflecting diverse stress-resilience mechanisms. Importantly, our findings demonstrate that high-throughput phenotyping at early seedling stages can capture divergent root dynamic strategies that may be predictive of later field performance under drought conditions. Overall, the integration of above- and below-ground phenotypic data with advanced analytical approaches extends trait assessment beyond traditional methods, providing deeper insights into root-shoot regulation under stress and supporting trait selection for crop improvement.