Ecosystem productivity data primarily from two forest census plots, NYO-03 and VEN-02, located in the Pastaza-Marañón Basin in Amazonian Peru. Site NYO-03 is a peatland pole forest, and Site VEN-02 is a palm swamp. The aim of the measurements was to estimate and compare rates of litter and root production and decay at the two sites, over a complete annual cycle, in order to understand the dynamics of carbon accumulation in peat in this region. Selected datasets extend to other sites, in order to provide some context for the measurements from NYO-03 and VEN-02. Downcore data from peat cores from the sites provide palaeoecological information. Full details about this dataset can be found at https://doi.org/10.5285/e34dc4c7-57d8-4120-921b-06d2f25d5e04