A whole plant gas exchange apparatus employs a chamber having a first region for accommodating a growth medium and a root system of a whole plant, and a second region accommodating a canopy of the plant. The regions are separated by a barrier, except for an opening through which the stem of the plant is accommodated. An air source supplies incoming air to the second region through an intake. An air outlet conveys outgoing air from the second region to a gas sensor for analysis of the outgoing air after photosynthetic interaction with the plant canopy. A vent communicates the first region of the chamber to an ambient environment outside the chamber. A resulting pressurized state of the second region is used to exhaust air from the first region through the vent in order to isolate this exhausted air from the analyzed canopy air.