The combined effects of chronic drought known in East Africa and demographic growth exacerbate the demand of water supply of the Republic of Djibouti. Moreover, the main water supply is from hard rock aquifers, and due to the scarcity of data and the lack of knowledge about the hydrogeological properties and aquifer geometry, the quantitative assessment of the available water resource is a tricky issue, related to a high level of uncertainty.**For identifying the main flow processes occurring in the volcanic aquifer system of Goda mountain range (Tadjourah region, 1600kmC, 52 surveys), groundwater flow simulations were carried out using an approach based on of the Generalized Likelihood Uncertainty Estimation (GLUE). This resulted in an ensemble of probably density functions describing the parameters and the corresponding uncertainties rather than a unique combination of parameters.**An estimation of the indirect recharge could be proposed, that corresponds to a major advance for the understanding of this crucial aquifer system, in particular its renewability. In addition, this work contributed to the development of an efficient numerical tool to assess impact of climate variability on the groundwater resources in arid zone.**