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The surface energy balance algorithm for land (SEBAL) has been successfully applied to estimate evapotranspiration (ET) and yield at different spatial scales. However, ET and yield patterns have never been investigated under highly heterogeneous conditions. We applied SEBAL in a salt-affected and water-stressed maize field located at the margin of the Venice Lagoon, Italy, using Landsat images. SEBAL results were compared with estimates of evapotranspiration by the Food and Agriculture Organization (FAO) method (ETc) and three-dimensional soil-plant simulations. The biomass production routine in SEBAL was then tested using spatially distributed crop yield measurements and the outcomes of a soil-plant numerical model. The results show good agreement between SEBAL evapotranspiration and ETc. Instantaneous ET simulated by SEBAL is also consistent with the soil-plant model results (R2 = 0.7047 for 2011 and R2 = 0.6689 for 2012). Conversely, yield predictions (6.4 t/ha in 2011 and 3.47 t/ha in 2012) are in good agreement with observations (8.64 t/ha and 3.86 t/ha, respectively) only in 2012 and the comparison with soil-plant simulations (8.69 t/ha and 5.49 t/ha) is poor. In general, SEBAL underestimates land productivity in contrast to the soil-plant model that overestimates yield in dry years. SEBAL provides accurate predictions under stress conditions due to the fact that it does not require knowledge of the soil/root characteristics.