The focus of this paper is on the pre-packaged version of SEBS in ILWIS and the sensitivity of SEBS to some parameters over which the user has some control when using this version of the model, in order to make informed choices to limit uncertainties. The sensitivities of SEBS to input parameters are related to daily ET rather than energy flux results since this is of interest to water managers and other users of the results of the SEBS model. This paper describes some of the uncertainties introduced by the sensitivity of the SEBS model to (a) land surface temperature and air temperature gradient, (b) the choice of fractional vegetation formula, (c) displacement height and the height at which wind speed is measured, and (d) study area heterogeneity. It was shown that SEBS is sensitive to land surface temperature and air temperature gradient and the magnitude of this sensitivity depended on the land cover and whether or not the wet-limit had been reached. The choice of fractional vegetation cover formula was shown to influence the daily ET results by up to 0.7 mm. It was shown that the height of the vegetation canopy should be considered in relation to the weather station reference height to avoid the sensible heat flux from becoming unsolvable due to a negative ln calculation. Finally the study area was shown to be heterogeneous although the resolution at which fluxes were calculated did not significantly impact on energy partitioning results. The differences in the upscaling from evaporative fraction to daily ET at varying resolutions observed implies that the heterogeneity may play the biggest role in the upscaling and the influence of albedo on this calculation should be studied.