Species composition in the present-day Amazonian heartland has an imprint of past marine influence. The exact nature, timing and extent of this marine influence, however, are largely unresolved. Here we use calcareous tests of foraminifera and marine palynomorphs from Miocene sediments in northwestern Amazonia to extend on current estimates for salinity ranges, paleoenvironments and paleogeography. Our samples mostly contain tests and/or organic linings of euryhaline (tolerant to a wide range of salinity) foraminifera of the genera Ammonia , Trochammina and Elphidium, with Ammonia being by far the dominant genus at all locations. Organic-walled dinoflagellate cysts (dinocysts), such as Spiniferites, Brigantedinium and Tuberculodinium vancampoae, are also common at a number of sites. This association of foraminifera and dinocyst taxa points at varying salinities, with aberrant forms of Ammonia indicating lower limits of 0-10 psu (practical salinity units) whereas dinocyst associations suggest more marine conditions. Such regional heterogeneity is common at the interface of shallow marine to freshwater environments, like estuaries. We conclude that during the early and middle Miocene marginal marine conditions reached at least 2000 km inland from the Caribbean portal. Global high sea level and fast subsidence in the sub-Andean zone are thought to be the controlling mechanisms of the marine incursions. Lowering of global sea level and a change in tectonic regime terminated the incursions in the course of the Plio-Pleistocene.