Spatiotemporal analysis to create accurate flood simulations in arid environments and hydrological unmeasured valley basins is one of the most important challenges in flood risk studies. This study investigated the flood risks that the torrents of the Wadi Thuwal Basin pose to the Haramain Train Pathway in various time and space scenarios. It also examined the potential impacts of climate change and environmental alterations on flood risks. The research aims to develop a comprehensive risk management plan that mitigates the possible negative consequences associated with floods. To achieve these goals, remote sensing, and high-resolution data from LiDAR, geological, topographic, and soil maps were processed using GIS. The Hydrological Engineering Center-Hydrologic Modeling System (HEC-HMS) was used to derive the hydrograph of torrential waters and the hydraulic model of the Hydrologic Engineering Center-River Analysis System (HEC-RAS) to simulate the Wadi Thuwal flood. This involved creating maps of torrential waters' velocity, depth, and spread, and evaluating the hydraulic installations under the train pathway. This study presents important planning considerations for policymakers in the KSA, given the paramount importance of the two holy cities of Makkah and Al-Madinah and the crucial role of the Haramain Train Pathway in ensuring safe connectivity between them.