One of the most damaging natural catastrophes is flooding; its effects on both human and natural resources are global. Desert River is an important landscape-shaping feature in semi-arid regions, and the river undergoes different processes, such as the bank full stage and water deficit, which are caused by the monsoonal flow and isolated torrential rainfall occurrence. The desert river Luni in western Rajasthan, India, offers distinctive hydrological conditions characterised by a mixture of structural, geomorphological, and anthropogenic settings. Even though the region is dominated by drought, floods are still a prominent phenomenon, occurring on a recurring scale. There is still a lack of systematic comparative study of the structural and anthropogenic differences, and for this reason, the nature of flood differs on the both banks of the river basin. By analysis, some of the important morphometric parameters like stream length, stream number, stream order, etc. The topographies, such as slope, Topographic Wetness Index (TWI), and Topographic Position Index (TPI), also the geological and geomorphological structure, cause the spatial dynamics of nature and causality of flood. The findings show that the two sides of the basin have different flood patterns. The area, especially the left bank tributary, is prone to flash floods due to its steeper gradient, high drainage density, and strong effect from the structural lineaments. Those floods are marked by a shorter duration and high magnitude of catastrophic floods, which are characterised by catastrophic rainfall, especially over the regions of Pali, Jalor, and Balotra. As well as the geomorphological setting and a well-integrated drainage system, which allows for fast runoff. On the other side, the right bank of the basin has its flatter terrain, lower drainage density, and interdune flow path, all of which contribute to lower runoff (topography and morphometric analysis). The right bank tributary is less intensive but lasts longer, and localised flooding will occur with limited reoccurrence. The anthropogenic alteration and urbanisation lead to the fast acceleration of runoff from building regions. Urban centres, such as Pali and Jalor, have changed natural drainage patterns, increasing the risk of catastrophic floods. On the other hand, natural landforms and climate have a greater influence on the flood regime of the right bank, whereas structural changes have less of an impact on water flow. The research highlights the complex interplay of geology, geomorphology, morphometry, topography, and human invention in shaping the dynamics of nature and flood causality in the Luni River. According to the riverbank, the detailed findings is contributed to an understanding of flooding in the arid region and underscore the basin-wise flood causality. Comparative analysis of the left and right bank tributaries offers valuable insights into regional flood potential, nature, and causality in the desert river system.