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The Karoonjhar mountainous area, situated at the southeast corner of Thar Desert, Pakistan, faces water scarcity most of the year due to erratic rainfall and limited groundwater resources. Though the area receives sufficient rainfall during the monsoon period, but water is not conserved in small dams and ponds for later use during the dry periods. One major challenge in implementing these runoffs harvesting techniques is the unavailability of data regarding runoff generation and lack of studies identifying suitable conservation sites. Looking at the gravity of the problem, the present study was conducted to delineate watersheds, quantify runoff, and identify potential runoff conservation sites in Karoonjhar mountainous area using remote sensing and GIS tools. Primary data was collected through ground trothing survey and soil sampling while secondary data about rainfall was obtained from Pakistan Meteorological Department (PMD). The 30-m resolution digital elevation model (DEM) was acquired from the Japan Aerospace Exploration Agency (JAXA). The data was processed in ArcGIS 10.3 and HEC-GeoHMS for the required objectives. The present study revealed that the probability of return period of a rainstorm of 52.5 mm was highest, i.e. 1.78 years. For a single rainstorm event of 52.5 mm, runoff generated at Karoonjhar mountainous area was about 7055 acre-ft (AF). Thirteen small watersheds with a total area of about 82314 acres were delineated for runoff harvesting. The curve number (CN) of the study area ranged from 54 to 100. Based on the historical rainfall data, runoff volume of about 21165 AF could be generated during the entire monsoon period. Results from the present study provide valuable information to water managers and decision makers that can be used to identify location and size of water harvesting structures such as small dams and ponds.