The discovery of large geometrical earthworks in interfluvial settings of southern Amazonia has challenged the idea that Pre-Columbian populations were concentrated along the major floodplains. However, a spatial gap in the archaeological record of the Amazon has limited the assessment of the territorial extent of earth-builders. Here, we report the discovery of Pre-Columbian ditched enclosures in the Tapajós headwaters. The results show that an 1800 km stretch of southern Amazonia was occupied by earth-building cultures living in fortified villages ~Cal AD 1250-1500. We model earthwork distribution in this broad region using recorded sites, with environmental and terrain variables as predictors, estimating that earthworks will be found over ~400,000 km2 of southern Amazonia. We conclude that the interfluves and minor tributaries of southern Amazonia sustained high population densities, calling for a re-evaluation of the role of this region for Pre-Columbian cultural developments and environmental impact.