The timing of continental-scale marine flooding events in Western Amazonia during the Neogene is still an unsolved question. Despite broad proxy-based evidence of such events, the pathways and duration of late Miocene marine incursions remain controversial. We provide coupled calcareous and organic microfossil and geochemical data from six onshore cores from Neogene sequences of the Solimões Basin, Brazil. Our records support minor marine influence in the early Miocene (23.0, 21.1, 18.6, and 16.3 Ma), middle Miocene (14.9, 13.7, and 12.9 Ma) and early Pliocene (4.7, 4.2–4.1, and 3.8 Ma), and conspicuous marine incursions in the late Miocene (11.1–8.8 Ma) suggested by the consistent presence of salinity-indicative microfossils and geochemical data. Our findings challenge the view of major marine incursions in the early and middle Miocene in the studied area. We propose for the first time a new late Miocene incursion (LMI) event as the main marine flooding event in Western Amazonia during the Neogene. These onshore records are compared with three offshore cores from the Atlantic and Pacific Oceans. The similarity between microfossil assemblages of the Solimões Basin and the Caribbean Sea, and evidence of increased runoff from the Orinoco river drainage system, strongly suggest the Caribbean Sea as the primary source area of the marine incursions, supporting a Venezuelan seaway. We further show for the first time the potential linkage between Neogene marine incursions (mainly the LMI) into the Solimões Basin and major disturbances in the global carbon cycle.