Changes in settlement patterns have influenced food-production systems and territorial organization in western Amazonia, and landing strips have affected current land-use patterns in indigenous territories in the region. In this study we characterize riverine and interfluvial production systems in the lower Pastaza River Basin in Ecuador, using historical ethnographic records, remotely sensed data, surveyed information, and statistical descriptions. Results show that nucleation of settlements around landing strips has increased indigenous people's control over their ancestral territories and changed the political and geographical landscape. At the same time, nucleation is slowly transforming indigenous livelihoods from mobile cultivation and foraging to sedentary farming. Even though indigenous communities will eventually become integrated into the national economy, the main elements of the traditional food-production system will likely remain the same. Development policies should respond to local land-management strategies in order to ensure the long-term sustainability of Amazonian socioecological systems.