Understanding energy and water balance processes in the Sandhills is crucial to assess the land–atmosphere feedback effects. The Sandhills located in western Nebraska covers a vast grassland ecosystem with limited variability in vegetation and soil. However, the combined effect of topography, land cover, and micrometeorology by subjecting the land surface to various disturbances and treatments is rarely studied. The NOAH Land Surface Model (LSM) was used to estimate net radiation, latent, sensible, and ground heat (GH) fluxes as well as water balance components for two growing seasons between 2005 and 2006 in various plots at the Grasslands Destabilization Experimental (GDEX) site where these plots were subjected to four different treatments and located at two topographical locations, namely high and low positions. The simulated results of net radiation and GH fluxes correlated well with measurements. While the amount of precipitation received was between 900 and 1000 mm for both seasons, on a daily and sub-daily time scale the partitioning of net radiation into latent, sensible, and GH fluxes showed high variability across the plots, primarily driven by vegetation and soil moisture. Total evapotranspiration and soil moisture averages suggested the influence of vegetation and the timing of precipitation also in controlling various land surface processes in the Sandhills. This study provides a framework for using the LSM to quantify the feedback effects and emphasizes the importance of microtopography and land treatments in the model environment. Copyright © 2009 John Wiley & Sons, Ltd.