About 30% of the Amazon Basin is covered by different wetland types that harbor a huge and unique biodiversity and provide essential ecosystem services. This study examines the floristic composition and diversity patterns of tree species in oligotrophic blackwater wetlands of two sub-basins, Abacate River in Central Amazonia and Falsino River in Eastern Amazonia, along a hydroedaphic gradient from the headwaters to the floodplains. Data collection involved nine 0.5 ha plots in each sub-basin, with monitoring of flood levels, water table depths over a year as well as soil properties. The diameter at breast height (DBH) ≥10 cm of all trees was obtained, and the species were identified. Regression models were used to relate floristic patterns to environmental gradients. Results showed distinct responses between sub-basins. Tree Alpha diversity in the Abacate River was influenced by hydroedaphic variation but not floristic composition. Conversely, floristic composition in the Falsino River was significantly explained by the hydroedaphic gradient, while alpha diversity was higher but not statistically significant. Local-scale heterogeneity drives floristic variation, leads to high species turnover, emphasizing the need for conservation strategies tailored to sub-basin-level dynamics.