Thousands of ancient agricultural terraced fields exist in ephemeral stream valleys in the central Negev desert. Their stone terrace walls captured runoff water, flowing from the surrounding hillslope catchments, to increase moisture in the loess soils of the terraced fields. Geoarchaeological research at the site of Horvat Haluqim discovered evidence for ancient farming and soil manuring in this arid desert region during various archaeological periods. Geographic Information Systems (GIS) and Digital Elevation Models (DEM) enable the development of hydrological models to investigate every ancient terraced field in a non-invasive manner, without disturbing the archaeological remains. We developed a GIS-based hydrological model, coupled with the D-Infinity (Tau DEM) algorithm, to evaluate annual runoff yields in 13 ancient terraced fields at the rural archaeological site of Horvat Haluqim. Our model precisely determined the runoff catchment area, ranging between 0.10 ha and 0.36 ha, of each individual terraced field. Supervised land cover classification, using Erdas Imagine, showed the surface percentages of crusted loess soil and exposed bedrock. Following an evaluation of runoff coefficients established by conventional hydrological studies in the region, we present results of model-calculated runoff overland flow yields. We modelled runoff amounts for each of the agricultural fields during an average year (1989–90) with 88 mm precipitation, a very wet year (1991–92) with 188 mm, and a severe drought year (1999–2000) with only 34 mm rainfall. Our initial results, based on an approximated average annual runoff coefficient of 10%, indicate that runoff water amounts during an average and wet rainfall year appear sufficient to grow agricultural crops in these ancient fields. However, drought years are of course more problematic. The modelling results are supported by the successful growth of trees in similar terraced wadi fields next to Horvat Haluqim, established by the Jewish National Fund. Given the inherent uncertainties involved in modelling, it is encouraging to note that the trees did survive also drought years. Our model may be applied to evaluate the effect of climatic changes on runoff water harvesting systems, looking back into the past and also to assess possible impact of future climate change scenarios in modern water harvesting projects.