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Airborne thermal infrared (TIR) imagery is a promising and innovative tool for assessing canopy response to a range of stressors. However, the expense associated with acquiring imagery for agricultural management is often cost-prohibitive. The objective of this study was to evaluate a less expensive system, an unmanned airvehicle (UAV) equipped with a TIR sensor, for detecting cotton (Gossypium hirsutum L.) response to irrigation and crop residue management. The experimental site was located on a 6.1 ha field in the Tennessee Valley Research and Extension Center located in Belle Mina, Alabama, where landscapes are gently rolling and soils are highly weathered Rhodic Paleudults. Treatments consisted of irrigation (dryland or subsurface drip irrigation) and crop residue cover (no cover or winter wheat (Triticum aestivum L.)). TIR (7 to 14 m) imagery was acquired on 18 July 2006 at an altitude of 90 m and spatial resolution of 0.5 m. Coincident with image acquisition, ground truth data consisting of soil water content (0-25 cm), stomatal conductance, and canopy cover were measured within a 1 m radius of each sample location. All sample locations were georeferenced using a real-time kinematic (RTK) GPS survey unit. Analysis of sample locations acquired in multiple flight lines was used to assess the stability and repeatability of the UAV system during an acquisition. Compared to field measurements of stomatal conductance with CVs ranging from 2% to 75%, variability in TIR emittance (CV < 40%) was within the observed tolerance of ground truth measurements of stomatal conductance. Significant differences in canopy cover and stomatal conductance across irrigation treatments allowed testing of the sensitivity of the UAV system. A negative correlation was observed between TIR emittance and stomatal conductance (r = -0.48) and canopy closure (r = -0.44), indicating increasing canopy stress as stomatal conductance and canopy closure decreased. TIR emittance exhibited greater sensitivity to canopy response compared to ground truth measurements, differentiating between irrigation and crop residue cover treatments. TIR imagery acquired with a low-altitude UAV can be used as a tool to manage within-season canopy stress.