This study aims to identify optimal rainwater harvesting (RWH) sites in the Al-Karak Basin, southern Jordan, with a focus on improving existing systems in arid and semi-arid regions (ASARs). These regions are increasingly affected by the impacts of climate change, including rising temperatures, declining rainfall, and higher evaporation rates. Such factors reduce water retention capacity and compromise the long-term effectiveness of RWH systems. Advanced analytical tools were employed to simulate runoff and generate RWH suitability maps, supported by detailed two- and three-dimensional (2D/3D) reservoir analyses. The Soil and Water Assessment Tool (SWAT) was calibrated and validated using observed discharge data from 2010 to 2017 using the SWAT-CUP tool. Calibration and validation results indicate robust model performance, with NSE and R2 values of 0.65 and 0.66 and 0.74 and 0.84, respectively. Seven key factors, such as slope, rainfall, drainage density, Terrain Roughness Index (TRI), land use/land cover, soil type, and lineaments, were combined using Geographic Information System (GIS) and the analytical hierarchy process (AHP). A composite suitability map was produced through weighted overlay analysis (WOA), identifying fifteen potential sites. These sites were further evaluated through hydromorphological assessments, 2D/3D terrain analysis, and SWAT model output. Parameters such as runoff, catchment size, and reservoir dimensions (height, width, surface area, and volume) were examined. Sites 1, 3, 4, and 7, including the existing Al-Karak Dam, emerged as the most promising RWH sites. Site selection accuracy was confirmed using receiver operating characteristic-area under the curve (ROC-AUC) analysis, yielding a strong predictive accuracy with an AUC of 0.79. The proposed methodology offers a practical and reproducible framework for strategic water resource planning and sustainable management of RWH structures in ASARs. Future research should incorporate high-resolution topographic data and socioeconomic variables to refine site selection criteria and enhance stakeholder engagement.