Sap flow sensors and other techniques are commonly used across species and plant organs to quantify water use and storage, detect stress, and evaluate the contribution of various tissues to plant/organ water balance. Sap flow methods often rely upon modelling or assumptions about how heat delivered by the sap flow sensors is partitioned into convection and conduction into active sapwood xylem and surrounding tissues. Dynamic changes in tissue water content over space and time can impact the interpretation of plant and organ water use and how various compartments contribute to an integrated response to plant stress. Here, we first summarize results from a variety of studies that used a combination of synchrotron-based X-ray microCT and MRI imaging to demonstrate how water content of various organs and xylem cell types can change temporally and how the spatial distribution of air-filled tissue may impact patterns of sap flow within the xylem network. Results from visualization techniques were compared to that from traditional hydraulic and sap flow methods to illustrate potential discrepancies particularly when comparing data from excised stems versus intact plants. Using a spatially explicit model, we demonstrate how changes in the water content of various cell types can impact resulting interpretation of sensor output. Implications for the interpretation of sap flow and other sensor data based on these results is discussed.