The Tanganyika continental rift basin is one of the most important structural features of the East African rift system and provides an opportunity to observe the early stages of rift basin development unobscured by postrift deformation and erosion. The geometry of half grabens and their zones of linkage have a great influence on rift development and depositional environments. Topographic features associated with zones of linkage between half grabens exert a direct control on drainage basin evolution, sediment supply, and synrift stratigraphy. Previous structural studies, based on widely spaced (~15 km) seismic reflection profiles, focused mainly on large-scale geometrical fault descriptions and not on the spatial and temporal linkage of the individual border faults controlling each half graben. In this article, using newly available basin age estimates, multichannel seismic reflection data, high-resolution single-channel sparker seismic data, and onshore structural data (remote directioning and microstructural field observations), we have constructed a detailed late Miocene-Holocene kinematic model for the evolution of the northern part of the Lake Tanganyika rift basin. A classification of fault interaction geometry is proposed to describe the initiation and development through time of major depocenters. Fault correlation lessons are provided for exploration seismic interpreters in extensional settings. The development of the depocenters of northern Lake Tanganyika is complex, and this article clearly shows that antecedent structures control subbasin initiation and development. As the rift evolves, border faults become dominant, producing more continuous and elongate depocenters, although the influence of transverse structures is still evident.