Noninvasive phenotyping can quantify dynamic plant growth processes at higher temporal resolution than destructive phenotyping and can reveal phenomena that would be missed by end-point analysis alone. Moreover, whole-plant phenotyping can identify germplasm and growth conditions that are optimal for both above- and below-ground tissues, and are important for efforts to breed more resilient and resource-efficient crops. However, noninvasive, dynamic phenotyping available today is generally expensive, complex, and non-modular. We developed a low-cost and versatile approach to non-invasively measure whole-plant performance over time by growing plants in isolated hydroponic chambers. We demonstrate the temporal and contextual versatility of our approach by measuring whole-plant biomass accumulation, water consumption, and water use efficiency every two days on unstressed and osmotically-stressed sorghum cultivars. In doing so, we identified relationships between root zone acidification and photosynthetic efficiency on whole-plant water use efficiency over time. Our system can be implemented using cheap, basic components and requires no specific technical expertise. It can, in theory, be used for any non-aquatic vascular plant species and for identifying more productive and resource-efficient crops.