In rift settings, the crustal stress field is dominated by extension, which leads to rift-parallel topography and basin alignments. However in some continental rift systems, some observables of the orientation of principal stresses show substantial deviations from these patterns. Such stress field rotations are currently poorly understood and could reflect the critical role of rift magmatism in the creation of topography, the plate state-of-stress, and volcanic and tectonic processes. Yet the role of magma intrusions, crustal thinning, and rift basin and flank topography on rift zone stress field rotations remain poorly quantified. The seismically- and volcanically-active Magadi-Natron-Manyara region of the East African Rift shows a 60∘ local stress field rotation with respect to regional extension. Here, we test the hypothesis that such rotation is due to the cumulative effects of surface and subsurface loads (lateral subsurface density contrasts). We use analytical and calibrated numerical models of magmatic rift zones to simulate lithospheric deformation in the presence of magma bodies, crustal thinning, and topography to quantify their effect on intrusions and fault kinematics in a rift setting. Our 3D static models of a weakly extended rift suggest that surface topography influences shallow stress localization, whereas subsurface density contrasts play a larger role in lower crustal stress localization. Both patterns suggest a preferred region for melt storage beneath the rift valley. We show that the interaction between topography, crustal thinning, extension, and a pressurized magma reservoir could generate principal stress orientations consistent with the local stress rotation observed from earthquake focal mechanisms. Our results demonstrate how rift topography and the geometry of crustal thinning can guide magmatism and strain localization, highlighting the need for a three-dimensional treatment of rift kinematics.