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Abstract The oldest structures in a rift basin define incipient rift architecture, and commonly modulate the patterns of landscape evolution, sedimentation, and associated hazards in subsequent phases of rift development. However, due to deep burial beneath younger, thick syn‐rift sequences, and limited resolution of seismic imaging, critical early‐rift processes remain poorly understood. In the Tanganyika Rift, East Africa, we augment existing 2‐dimensional (2‐D) seismic reflection data with newly acquired aeromagnetic and Full‐Tensor Gradiometry data to assess the deep basin and underlying basement structure. Aeromagnetic and gravity grids show a dominance of NW‐trending long‐wavelength (>5 km) structural fabrics corresponding to the deeper basement, and dominant NW‐trending with a secondary NNE‐trending shorter‐wavelength (<3 km) fabric representing shallower, intra‐basin structures. Seismically‐constrained 2‐D forward modeling of the aeromagnetic and gravity data reveals: (a) an anomalously high‐density (2.35–2.45 g/cc) deep‐seated, fault‐bounded wedge‐shaped sedimentary unit that directly overlies the pre‐rift basement, likely of Mesozoic (Karoo) origin; (b) ∼4 km‐wide sub‐vertical low‐density (2.71 g/cc) structures within the 3.2 g/cc basement, interpreted to be inherited basement shear zones, (c) early‐rift intra‐basin faults co‐located with the modeled shear zone margins, in some places defining a persistent structurally‐controlled intra‐basin “high,” and (d) a shallow intra‐sedimentary V‐shaped zone of comparatively dense material (∼2.2 g/cc), interpreted to be a younger axial channel complex confined between the intra‐basin “high” and border fault. These results provide new insight into the earliest basin architecture of the Tanganyika Rift, controlled by inherited basement structure, and provide evidence of their persistent influence on the subsequent basin evolution.