We describe here the first autonomous permanent deep lakes found in the Amazon lowlands. Permanent Amazon lakes have hitherto been considered unlikely because the ubiquitous rivers meandering over flat terrain should obliterate ancient basins, resulting in lakes subject to annual flooding, the so-called ‘varzeas’1–4. The lakes described here are in the rain forests of Ecuador in western Amazonia, within 100 km of the Andes mountains, but at elevations below 700 m (Fig. 1). They occupy either deep abandoned channels of high-energy rivers or closed volcanic basins. Sedimentary histories and pollen data over several millennia from these lakes record disturbance of the Amazonian ecosystem by flooding, encouraging the view that high Amazonian species-richness is maintained by non-equilibrium processes5,6.