Study areaSouthern Sections of Western Afar rift margin and associated rift floor. Study focusThe purpose of this study is to identify the source and mechanisms of groundwater recharge based on geological, hydrochemical, and environmental isotope studies. New hydrogeological insightsThe investigation illustrate that the columnar jointed basalt was extended from the plateau to the rift margin. In addition, transverse structures trending NW-SE and NE-SW connect the plateau to the rift margin and the marginal grabens to the rift floor. The hydrochemical interpretations with EC and TDS shows that the groundwater from the plateau has evolved from Ca-dominated and slightly mineralized to Na-dominated and highly mineralized to the rift floor. Isotopically, the deep groundwater systems are depleted in the entire physiography in contrast to the shallow groundwater systems. Radon measurements are higher at the outlets of the marginal grabens and between the rift margin and the rift floor, suggesting groundwater feeds the river. A comprehensive analysis of the aforementioned results suggests that the deep circulating groundwater is recharged in the plateau and escarpment and chemically altered with increasing depth and along its preferential flow path into the rift floor. Therefore, the plateau area is the main source of recharge for the western Afar rift margin and associated rift floor, due to the presence of preferential pathways, mainly the columnar jointed basalts and cross-structures.