Abstract The water balance of the upper Nile swamps, in particular, the Sudd, has been the topic of debate for many years. Surface Energy Balance Algorithm for Land (SEBAL) is a parameterization scheme of surface heat fluxes based on spectral satellite measurements. The SEBAL scheme has been applied to derive the energy balance components from National Oceanic Atmospheric Administration-Advanced Very High Resolution Radiometer (NOAA-AVHRR) images over the extensive swamps in the upper Nile. The study area covers the swamps of the Sudd, Bahr el Ghazal and the Sobat sub-basins. The actual evaporation and soil moisture for an area between 2–12°N and 26–36°E (approximately 1000 km×1000 km) have been investigated. Monthly (actual) evaporation and soil moisture maps for the year 2000 have been generated. The evaporation results were verified against longer-term averaged rainfall and flow data of the three sub-basins. A close resemblance was obtained for the Sudd (1.8% error) and the Sobat Basin (5.7% error), while the balance lacks closure for the Ghazal basin (27%) due to un-gauged or inadequately gauged inflow from the upper catchments. It is concluded that soil moisture availability controls the monthly evaporation rates for all areas that are not saturated with water, and that a significant dry-down in the winter period occurs. It is concluded that the evaporation for the Sudd wetlands is 20% less and the average area occupied by the wetlands is 74% larger than assumed in earlier hydrological studies (e.g. Jonglei canal studies). The derived results can serve as a sound basis to support the widely debated evaporation losses from the Sudd, as well as form an input to regional scale climate models for studying atmospheric circulation patterns over Africa and the Nile Basin.