Assessing patterns of abundance and distribution of Amazonian species is still an overwhelming task that requires integration of multiple disciplines. This work is based on background information gathered from previous reconstructions of the geological history of the lower Amazon drainage basin, in order to analyse biodiversity patterns within the context of landscape transformation. A highly dynamic geological scenario is depicted for this area during the Plio-Pleistocene and Holocene, which consisted of a large palaeovalley formed as a response of tectonic reactivation. This palaeovalley was filled with sediments transported by a north/northwest orientated palaeo-Tocantins River. The palaeodrainage became abandoned as the main river course was deviated to the northeast, initiating the separation of Marajó Island from mainland. Geology had a direct impact on the modern physiognomy, with open vegetation dominating in areas with Holocene sedimentation, while closed forests prevailing in older Quaternary and, probably also, Pliocene terrains. Data from fossil and modern mammalian groups indicate the connection of Marajó Island to the mainland during the Last Glacial Maximum, when open vegetation seems to have dominated. Tectonic subsidence was responsible for the maintenance of this vegetation pattern on the eastern side of the Marajó Island, keeping it as a habitat favourable for savanna adapted faunal elements. Based on this kind of information, this work attempts to highlight the importance of integrating studies combining geological and biological events as the key to understand biodiversity patterns in Amazonia. It is expected to open new lines of research dealing with the comprehension of ecology, species and genetic diversity, biogeography, evolutionary scenarios, and speciation mechanisms.