The conservation of tropical forests has become an important mechanism for the mitigation of the negative effects of climate change. Countries located in the Neotropical region, Central and South America, are aiming to understand the drivers of carbon stocks of their forests to build a better capacity for forest management. In this study, we calculated Above Ground Biomass – AGB stocks for 32 (1 ha) vegetation plots of forests classified as terra firme and seasonally flooded, and evaluated the effect of basin location, structural and environmental variables on the magnitude of AGB stocks. We report that variation among river basins results from the effects of fragmentation and soil fertility. The most important variable, determining the magnitude of AGB stocks in lowland forests in the region is the number of large trees per hectare. Seasonally flooded forests should be studied and managed separately from terra firme forests as these behave differently in the relationship between tree species diversity and AGB stocks. We found that the proportions of endozoochoric and synzoochoric tree species are important variables for the magnitude of AGB stocks in these forests. We present the first account on the drivers of AGB stocks in Northwestern South America and show that environmental characteristics of forests, such as flooding and fragmentation should be taken into account to determine the variation on AGB stocks among forests in this region.