Controlled environment chambers are an important research tool to quantify canopy level phototsynthesis under controlled temperatures. Because the chambers are isolated from the atmosphere, fluxes of CO2 and water vapor in and out of the chamber are minimized. This allows for precise measurement of CO2 assimilation rates to quantify photosynthesis as CO2 can be easily metered and measured. The measurement of water fluxes is often carried out by measuring condensate draining from cooling coils and depends on maintaining a constant humidity in the chambers. This provides a direct measure of evapotranspiration. However, in growth chambers with soil bins, this does not give information on root activity with soil depth. In this study we instrumented the soil bins with time domain reflectometry probes that were controlled by an automated system. The soil water content was monitored once an hour at five vertical depths with three measurement locations per depth. The differences between the methods were larger when the plants were small and decreased as canopy cover increased. Differences in estimated transpiration between the two methods also depended on which layers in the soil contributed toward water uptake. The changes in soil water content lagged behind the changes in water accumulated from the cooling coils by about 1 hour. Overall, the differences between the methods were on the order of about 1 to 2 liters per day and less (for a 1 m2 area).