- Abstract Discrepancies can arise among surface flux measurements collected using disparate techniques due to differences in both the instrumentation and theoretical underpinnings of the different measurement methods. Using data collected primarily within a pair of irrigated cotton fields as a part of the 2008 Bushland Evapotranspiration and Remote Sensing Experiment (BEAREX08), flux measurements collected with two commonly-used methods, eddy covariance (EC) and lysimetry (LY), were compared and substantial differences were found. Daytime mean differences in the flux measurements from the two techniques could be in excess of 200 W m −2 under strongly advective conditions. Three causes for this disparity were found: (i) the failure of the eddy covariance systems to fully balance the surface energy budget, (ii) flux divergence due to the local advection of warm, dry air over the irrigated cotton fields, and (iii) the failure of lysimeters to accurately represent the surface properties of the cotton fields as a whole. Regardless of the underlying cause, the discrepancy among the flux measurements underscores the difficulty in collecting these measurements under strongly advective conditions. It also raises awareness of the uncertainty associated with in situ micrometeorological measurements and the need for caution when using such data for model validation or as observational evidence to definitively support or refute scientific hypotheses.