Thar desert spreads in western part of Rajasthan, northern part of Gujarat, and some parts of Punjab and Haryana. The terrain is dominated by slightly sloping plains, broken by some dunes and low barren hills. The area is characterized by low average annual rainfall which is erratic in distribution and intensity. Drought will remain a major hindrance for agricultural production in Thar desert. Due to water stress condition, many watershed based development activities has been adopted by government and non-government organizations for the growth and sustainable development of this region. The need of this hour is preparation of a national level watershed atlas of 1:50,000 scale because majority of thematic maps are being produced presently on same or 1:10,000 scale. The manual delineation of watershed boundary in flat terrain based on topographic map will be time consuming and less accurate in the absence of prominent contour lines. Automated approach for watershed delineation using Digital Elevation Model (DEM) along a suitable algorithm has the advantage because the output is not only less time consuming but also independent from human decisions. Hence, a case study has been carried out in Churu sub-basin part of Indus basin which is located in Thar desert region. Depression less DEM with different spatial resolutions was used as input in hydrology tool of ArcGIS spatial analyst function for characterization of watersheds. The Churu sub-basin has been divided into various numbers of watersheds with an average size of 600 km2. These watershed boundaries have been validated with respect to high resolution satellite imageries (IRS P6 LISS IV), Survey of India toposheets, ancillary data and limited field checks.