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During the development of continental rifts, strain accommodation shifts from border faults to intra-rift faults. This transition represents a critical process in the evolution of rift basins in the East African Rift, resulting in the focusing of strain and, ultimately, continental breakup. An analysis of fault and fluid systems in the younger than 7 Ma Natron and Magadi basins (Kenya-Tanzania border) reveals the transition as a complex interaction between plate flexure, magma emplacement, and magmatic volatile release. Rift basin development was investigated by analyzing fault systems, lava chronology, and geochemistry of spring systems. Results show that extensional strain in the 3 Ma Natron basin is primarily accommodated along the border fault, whereas results from the 7 Ma Magadi basin reveal a transition to intra-rift fault–dominated strain accommodation. The focusing of strain into a system of intra-rift faults in Magadi also occurred without oblique-style rifting, as is observed in Ethiopia, and border fault hanging-wall flexure can account for only a minor portion of faulting along the central rift axis (∼12% or less). Instead, areas of high upper crustal strain coincide with the presence of hydrothermal springs that exhibit carbon isotopes and N2-He-Ar abundances indicating mixing between mantle-derived (magmatic) fluids and air saturated water. By comparing the distribution of fault-related strain and zones of magmatic fluid release in the 3 Ma Natron and 7 Ma Magadi basins, we present a conceptual model for the evolution of early-stage rifting. In the first 3 m.y., border faults accommodate the majority of regional extension (1.24–1.78 mm yr–1 in Natron at a slip rate ranging 1.93–3.56 mm yr–1), with a significant portion of intra-rift faulting (38%–96%) driven by flexure of the border fault hanging wall. Fluids released from magma bodies ascend along the border fault and then outward into nearby faults forming in the flexing hanging wall. By 7 m.y., there is a reduction in the amount of extension accommodated along the border fault (0.40–0.66 mm yr–1 in Magadi at a slip rate ranging from 0.62 to 1.32 mm yr–1), and regional extension is primarily accommodated in the intra-rift fault population (1.34–1.60 mm yr–1), with an accompanying transition of magmatic volatile release into the rift center. The focusing of magma toward the rift center and concomitant release of magmatic fluids into the flexing hanging wall provides a previously unrecognized mechanism that may help to weaken crust and assist the transition to intra-rift dominated strain accommodation. We conclude that the flow of magmatic fluids within fault systems plays an important role in weakening lithosphere and focusing upper crustal strain in early-stage continental rift basins prior to the establishment of magmatic segments.