The eastern Brazilian coastal drainages are of great biogeographical significance, because of their highly endemic fish faunas. Phylogenetic patterns suggest a close biotic relationship between the rivers that flow into the Atlantic and those on the adjacent upland crystalline shield. However, little has been said on the dynamics of the geological processes causally related to the cladogenetic events between these areas. Distributional and phylogenetic patterns suggest a close association with the geological history of the passive continental margin of South America, from the Cretaceous to the present day. In this area megadome uplifts, rifting, vertical movements between rifted blocks and the erosive retreat of the South American eastern continental margin are hypothesized as the main geological forces controlling the distribution of freshwater fishes. The tectonic activity associated with the break-up of Gondwana and separation of South America and Africa formed six megadomes that control most of the current courses of the main crystalline shield river basins. Except for basins located at the edges of such megadomes, these river systems developed long, circuitous routes over the ancient Brazilian crystalline shield before emptying into the recently opened Atlantic Ocean. Initial cladogenetic events between upland crystalline drainages and Atlantic tributaries were probably associated with vicariant processes, and some ancient basal sister-groups of widespread inclusive taxa are found in these coastal hydrographic systems. Later, generalized erosive denudation resulted in an isostatic adjustment of the eastern margin of the platform. These, along with reactivations of ancient rifts led to vertical movements between rifted blocks and gave rise, in southeastern Brazil, to taphrogenic (rift related) basins. These basins, such as the Taubaté, São Paulo, Curitiba and Volta Redonda basins, among others, captured adjacent upland drainages and fauna. The fossil fishes from the Tremembé Formation (Eocene-Oligocene of Taubaté Basin) exemplify this process. Other taphrogenic systems of Tertiary age were also identified in other segments of the Atlantic continental margin, such as in Borborema province, in NE Brazil, with marked influence over drainage patterns. At the same time, erosive retreat of the eastern margin of the platform successively captured upland rivers, which became Atlantic tributaries evolving associated to main rift systems. The continued nature of these processes explains the mixed phylogenetic and distributional patterns between Atlantic tributaries and the upland crystalline shield areas, especially in the southeastern continental margin, represented by successively, less inclusive sister-groups associated with cladogenetic events from the Late Cretaceous to the present.