This study aims to investigate groundwater recharge and flow patterns in tectonically active rift systems, exemplified by a case study in the Main Ethiopian Rift. The chosen approach includes the investigation of hydrochemical parameters and environmental isotopes (³H, δ²H, δ¹⁸O, δ¹³C-DIC, ¹⁴C-DIC, ⁸⁷Sr/⁸⁶Sr). Apparent groundwater ages were determined by radiocarbon dating after correction of ¹⁴C-DIC using a modified δ¹³C-mixing model and further validation using geochemical modelling with NETPATH. Hydrochemical and isotopic data indicate an evolutionary trend existing from the escarpments towards the Rift floor. Groundwater evolves from tritium-containing and hence recently recharged Ca–HCO₃-type water on the escarpments to tritium-free Na–HCO₃ groundwater dominating deep Rift floor aquifers. Correspondingly, rising pH and values coupled with increasingly enriched δ¹³C signatures point to hydrochemical evolution of DIC and beginning dilution of the carbon isotope signature by other carbon sources, related to a diffuse influx of mantle CO₂ into the groundwater system. Especially thermal groundwater sampled near the most recent fault zones in the Fantale/Beseka region displays clear influence of mantle CO₂ and increased water–rock interaction, indicated by a shift in δ¹³C and ⁸⁷Sr/⁸⁶Sr signatures. The calculation of apparent groundwater ages revealed an age increase of deep groundwater from the escarpments to the Rift floor, complying with hydrochemical evolution. Within the Rift, samples show a relatively uniform distribution of apparent ¹⁴C ages of 1800 to 2800 years, with the expected down-gradient aging trend lacking, contradicting the predominant intra-rift groundwater flow described in existing transect-based models of groundwater flow. By combining hydrochemical and new isotopic data with knowledge of the structural geology of the Rift, we improve the existing groundwater flow model and propose a new conceptual model by identifying flow paths both transversal and longitudinal to the main Rift axis, the latter being strongly controlled by faulted and tilted blocks on the escarpment steps. The connection between groundwater flow and fault direction make this model applicable to other active rift systems with similar structural settings.