This dataset is a compilation of carbon and energy eddy covariance flux, meteorology, radiation, canopy temperature, humidity, CO2 profiles and soil moisture and temperature profile data that were collected at nine towers across the Brazilian Amazon. Independent investigators provided the data from a variety of flux tower projects over the period 1999 thru 2006. This is Version 2 of the tower data compilation, where the data have been harmonized across projects, additional quality control checks were performed, and have been aggregated to hourly, daily, 16-day, and monthly timesteps. This integrated dataset is intended to facilitate integrative studies and data-model synthesis from a common reference point.