Increasingly, archaeological research in Amazonia is revealing complex precolonial occupation in areas around riverine confluences. In 2014, the first site-based archaeological investigations were undertaken in Gurupá, Pará, Brazil, a municipality that spans the region of the Xingu-Amazon confluence. The Portuguese controlled access to Amazonia from 1623 onward through a network of settlements organized around Gurupá. Results from extensive excavations of terra preta sites, landscape archaeology, and analysis of ceramic evidence suggest that this was also a precolonial crossroads. Carrazedo, once a booming historical town (Arapijó), sits atop a significantly larger terra preta site. Excavations in historical and precolonial sectors of Carrazedo found well-preserved remains, including a precolonial house terrace complex. The extent of terra preta and earthworks at Carrazedo indicate that the precolonial occupation was more intensive than the colonial-historical period occupation. Regional survey revealed colonial-historical period sites consistently overlying expansive precolonial sites, the density and extent of which suggest a major precolonial center at the Xingu-Amazon confluence. Overall, ecological and landscape modifications appear to have been more intense in the precolonial past than during later periods. Short- and long-distance settlement networks also differed during the two periods. This as-of-yet understudied region promises to shed new light on deep-time human-environment interactions and spatial organization in the humid tropics of Amazonia.