Indigenous territories and protected areas are crucial for ecosystem connectivity in the Amazon basin.

Ecosystem connectivity-the uninterrupted flow of natural processes within and among ecosystems-is critical for maintaining healthy ecosystem functions. However, in the Amazon drainage basin, multiple anthropogenic activities are rapidly disrupting connectivity. To assess the severity of this problem, we analyzed the spatial distributions of six major anthropogenic activities: dam construction, deforestation, fire, mining, oil and gas exploitation, and roads. We examined their impacts across four key landscapes: Amazonian Andes, lowland nonflooded forests, wetlands, and rivers. Using a resistance-based connectivity model, we quantified connectivity across terrestrial, wetland, and river ecosystems and found a marked decline in connectivity across the basin. A central focus of our study was the role of Indigenous Territories and Protected Areas (ITPAs), which collectively cover over 50% of the basin. Our findings show that ITPAs sustain significantly high levels of ecosystem connectivity. Only 14 to 16% of ITPA land is impacted by anthropogenic activities, compared to 38% in unprotected areas. Terrestrial ecosystems in the southern and eastern Amazon are heavily impacted by deforestation, mining, and fires, with significantly higher connectivity inside ITPAs than in unprotected areas ( < 0.01). Wetlands and riverine ecosystems also face severe fragmentation, particularly from dams and illegal mining-but maintain stronger connectivity within ITPAs (wetlands: < 0.01; rivers: < 0.001), with the few remaining free-flowing Andean rivers increasingly isolated from the lowland Amazon. Strengthening governance and sustainable initiatives in ITPAs, in partnership with local inhabitants, represents an expedient, efficient, and cost-effective strategy for conserving ecosystem connectivity in the Amazon basin.