A wide variety of aquatic vertebrates from fluvio-lacustrine facies of northern South America (Colombia and Venezuela) have been used as unequivocal evidence to support hydrographic connections between western Amazonia and the Proto-Caribbean Sea during the Miocene. By the end of the Miocene, changes in the major hydrographic systems of the region produced losses of habitats and a regional faunal turnover, as has been documented in the geological record of the Urumaco region. Here, we report a new Tortonian aquatic and terrestrial vertebrate assemblage from two localities of the Caujarao Formation (El Muaco Member) in western Venezuela. The vertebrate assemblage includes a gharial (cf. †Gryposuchus pachakamue), alligatorid crocodylians (†Purussaurus and Alligatoridae indet.), a freshwater turtle (Chelus sp.), snakes (cf. Eunectes sp.), serrasalmids and pimelodids and thorny catfishes, a rodent (†Potamarchus sp.), pampatheres (†Scirrotherium sp.), sloths, as well as plant remains (coal and amber). Although the Caujarao Formation has been referred to as a fully marine environment, the new assemblage reported here suggests a freshwater input to the coastal area. Taxonomic and biogeographic affinities between the Muaco Member community and that reported from the Miocene proto-Amazonian systems are indicative of the persistence of ecological and hydrographic continuity at minimum until the end of the Miocene in at least an area of northwestern South America.