Technical Abstract: Plant-available water in desert riparian forests is very heterogeneously distributed in space and time. Up-scaling tree transpiration in these systems is necessary for determining riparian water balance and the amount of water required to sustain forest structure and function. Rates of transpiration (E) were evaluated in desert riparian cottonwood (Populus fremontii) stands at perennial and intermittent reaches of the San Pedro River in southeastern Arizona, one of the last free-flowing rivers in the arid Southwest. Sap flow was measured using thermal dissipation probes and scaled to the stand level to investigate E in relation to canopy structure, depth to groundwater (GW) and vapor pressure deficit (D). The cottonwood stand located at the perennial stream site had higher leaf area-to-sapwood area ratio (0.31 ± 0.04 m2 cm-2), leaf area index (2.75) and shallower GW (1.1 to 1.8 m) than the stand at the intermittent stream site (0.21 ± 0.04 m2 cm-2, 1.75 and 3.1 to 3.9 m, respectively). Moreover, total annual E was higher at the perennial stream site (966 mm) than at the intermittent stream site (484 mm). The significant positive correlation between E and D indicates high hydraulic conductance along the root-shoot pathway of cottonwood trees at the perennial stream site. During the peak dry period prior to the monsoon season, the cottonwood stand at the intermittent stream site exhibited midday depression in stomatal conductance in response to high D (mean max D = 6 kPa). However, E increased with no apparent stomatal closure at midday (mean max D = 5 kPa) after significant monsoonal rains and runoff events that recharged groundwater at both sites. Riparian cottonwood forests exist across a continuum of groundwater availability and their access to shallow groundwater sources determines structural and physiological responses to drought. Increases in water table depth will enhance the susceptibility of these forests to drought stress, which may threaten their productivity