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[1] A terrestrial ecosystem model (integrated biosphere simulator (IBIS)) and a hydrological routing algorithm (HYDRA) are used in conjunction with long time series climate data to simulate the river discharge and flooded area of the Amazon/Tocantins River basin over the last 60 years. Evaluating the results of this modeling exercise over the entire basin yields three major results: (1) Observations at 121 stations throughout the basin show that discharge is well simulated for most tributaries originating in Brazil. However, the discharge is consistently underestimated, by greater than 20%, for tributaries draining regions outside of Brazil and the main stem of the Amazon. The discharge underestimation is most likely a result of underestimated precipitation in the data set used as model input. (2) A new flooding algorithm within HYDRA captures the magnitude and timing of the river height and flooded area in relatively good agreement with observations, particularly downstream of the confluence of the Negro and Solimões Rivers. (3) Climatic variability strongly impacts the hydrology of the basin. Specifically, we find that short (∼3–4 years) and long (∼28 years) modes of precipitation variability drive spatial and temporal variability in river discharge and flooded area throughout the Amazon/Tocantins River basins.