Land-use changes have altered the dynamics, structure and functioning of semideciduous seasonal forests in the Amazonian agricultural frontier. Such changes impact local and regional climate through disruptions of hydrological, carbon and energy cycles, with cascading effects that threaten regional biodiversity and the health of streams. Although these effects persist for decades, and interact with global climate changes, the possible trajectories of forests and aquatic environments remain poorly understood in the Amazon agricultural frontier, as well as its impacts on biodiversity and ecosystem services and functions it performs. This is largely due to the lack of studies capable of assessing the extent to which terrestrial and aquatic ecosystems are changed within fragmented landscapes and under high pressure of large-scale agricultural in the long-term. We aim to answer the following questions: (1) What are the long-term impacts of the interaction among forest fragmentation, climatic extremes and fire disturbances in the structure, diversity and functioning of Amazon-Cerrado transitional forests? (2) To what extent are the forests located on the agricultural frontier resilient to multiple disturbances, and what are the consequences for ecosystem processes and for local and regional biodiversity? (3) Are deforestation and degradation of tropical forests already changing the balance of water and energy much faster than expected, due to increased greenhouse gas emissions? Such changes would be higher during a dry season and years of severe drought? Are deforestation and land-use change modifying the hydrological regime in the basin scale? How these changes affect ecosystem processes of terra-firme forests, and how they would affect riparian forests? (4) What are the roles of riparian forests in maintaining the integrity of ecosystems in agricultural landscapes?