This study presents a multi-disciplinary approach for the hydrogeological assessment and characterization of water resources in typical arid and semi-arid areas with high anthropogenic pressure, and where environmental conditions and political context prevent extensive field surveys. The use of a three-dimensional (3D) hydrogeological conceptual model, integrating hydrochemical and multi-isotope data, is proposed for the Batna and Biskra area (NE Algeria).Geological data were assembled in 3D geological software, from which a 3D hydrogeological conceptual model was constructed, which included the delineation of groundwater flow directions. The isotopic characterization, including deuterium and oxygen isotopic composition of water (δ2H and δ18O), and tritium (3H), provided information regarding recharge sources, flow pathways and residence times of groundwaters. Hydrochemical parameters, measured on the same samples, supported the interpretation of isotope data. All data were processed in a geographic information system (GIS) environment. The effectiveness of this approach was tested on a complex system of aquifers with high hydrogeological heterogeneity. Results show the important role the tectonic setting of an area can play in the hydrogeology and hydrochemistry of its principal groundwater systems. The fault network in the study region connects different aquifers, resulting in the mixing of groundwaters. The region most influenced by geological structures is the southern part of the study area, close to Biskra city. In fact, besides a limited contribution of recharge from rain and surface water derived from flood events, the recharge of the Cenozoic aquifers seems to proceed from the ascension of deeper Cretaceous groundwaters through the fault network, as indicated by temperature, bulk chemistry and in particular δ2H, δ18O and 3H results. In contrast, results suggest that the recharge of the low mineralized Maastrichtian waters is primarily influenced by local precipitation and runoff in the mountainous northern part of the study area. Tritium content, low salinity, and bulk chemistry all suggest such waters to be a mix of pre-bomb (deeper flow-lines within the aquifer) and recent water, with no contribution from the deepest Continental Intercalaire groundwaters.The proposed approach reduces ambiguity about the studied aquifer systems, greatly improves the conceptual understanding of their behaviour, and could provide insights into the vulnerability of the aquifers to different anthropogenic pollution phenomena. The methodology used appears to be a valid tool that could be applied to other geographical areas, to inform the design and implementation of efficient management strategies aimed at improving the quality and availability of water resources. Moreover, three-dimensional modelling methods are becoming increasingly applied to different aspects of groundwater management, to obtain a detailed picture of subsurface conditions.