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The taxonomic composition and palaeoecological signature of molluscan faunas from the Miocene Pebas Formation of Peruvian Amazonia are assessed. The Pebas fauna is almost entirely made up of extinct, obligate aquatic taxa, and is dominated in numbers of species and specimens by endemic cochliopine hydrobiid gastropods and pachydontine corbulid bivalves. Molluscan assemblages are defined and linked to depositional environments. Isotope data from the shells indicate freshwater settings during deposition of the Pebas Formation, with the exception of a few incursion levels that were deposited under oligohaline-mesohaline conditions. Faunal and isotope geochemical data point to a large, long-lived freshwater lake system at sea level with swamps and deltas, open to marine settings in the north (Llanos Basin). Sedimentological data and ichnofossils point to (restricted) marine settings. These different interpretations are discussed, and it is concluded that faunas (including ichnofabrics) from evolutionary isolated and longlived systems cannot be assessed in a straightforward actualistic mode, using taxa from non-long-lived environments for comparison. Aspects of Lake Pebas are compared with modem depositional environments. Lake Pebas is among the largest and longestlived lake complexes in Phanerozoic history; it was an important stage for the evolution of endemic molluscan and ostracod faunas. It may have played some role in the transition of marine biota to Amazonian freshwater environments during the Miocene, and likely was an important, hitherto unrecognised, dispersal barrier for terrestrial organisms in northwest …