A controlled environment system, termed the Phyto-Nutri-Tron (PNT), has been established to study whole plant ecophysiological responses to multiple environmental factors. The PNT is a computer-controlled highly flexible growth facility with independent control of the shoot and the root environment. The facility consists of two growth cabinets each containing four separate hydroponic growth systems. The growth cabinets can be used as assimilation chambers with individual control of temperature, humidity, light, CO2 and monitoring of O2. The hydroponic growth systems are connected to nutrient supply units with disinfection systems and individual control of temperature, pH and oxygen. The ionic composition of the solutions has automated feedback control through a PO4 autoanalyzer and a flow injection analyzer which also analyzes NH4+, NO2- and NO3-. Other ions are automatically monitored by ICP-AES. The system has automated calibration procedures of the analytical equipment and prolonged studies of plant growth can be performed under constant environmental conditions. This paper describes the design and construction of the PNT, the results of a number of tests showing the degree of control of environmental factors and the results of a comparative study on NH4+ and NO3- uptake kinetics by Juncus effusus conducted in the PNT demonstrate the use of the PNT in ecophysiological studies.