Extensive areas covered by semi-permanent water bodies were common during the Miocene in the Neotropics. These floods are noteworthy because of their possible role in promoting the high biological diversity observed today in the Amazonia. In particular, a relatively good understanding of the floods has been achieved for the Llanos basin of Colombia and western Amazonia. In these two basins the evidence suggests episodes of marine incursions and development of lacustrine systems at different times during the Miocene. Other intra-montane basins in Colombia, like the Middle and Upper Magdalena basins, also show clear evidence that water bodies covered them during that time. However, the chronostratigraphy and paleoecology of these deposits are still unclear. In this study, we use the palynological record of the Middle and Upper Magdalena valleys to establish the age of the deposits of the Barzalosa Formation, a unit that preserves a detailed record of a lacustrine system deposited during the late early Miocene in the Upper Magdalena Valley. The results indicate that the Barzalosa Formation is correlative with the lacustrine deposits of the La Cira fossiliferous horizon in the Middle Magdalena Valley. This indicates that extensive lacustrine systems covered the intramontane basins of the northern Andes during the early Miocene. Paleoecologically, the Barzalosa Formation is the result of the evolution of a lacustrine system in three phases, which show marked differences in the proportion of algae, palynological composition and sedimentary depositional sequence. Climate and tectonic processes were the most probable mechanisms controlling the evolution of the Barzalosa system.