Climate is a strong determinant of tropical forest productivity; therefore, it is often assumed that Amazonian forest growing on the same local rainfall regime responds similarly to fluctuations in rainfall, independently of soil differences among them. We evaluated intra- and inter-annual variation of net primary productivity (NPP) components, and forest dynamics during 2004–2012 yr in five forests on clay, clay-loam, sandy-clay-loam, sandy-loam and loamy-sand soils, and the same local rainfall regime in northwestern Amazonia (Colombia). The questions were as follows: (1) Do NPP components and forest dynamics respond synchronously to temporal rainfall fluctuations? (2) Are the responses between above and belowground components and forest dynamics similar for different forest stands? A slight and complex synchronicity among different NPP components in their response to temporal rainfall fluctuations were found; few plots showed that aboveground biomass (AGB) and stem growth were susceptible to rainfall fluctuations, while belowground components (fine roots) showed correlation with one-month lagged rainfall. Furthermore, despite that northwestern Amazonia is considered relatively aseasonal, litterfall showed high seasonality in the loam-soil forest group, as well as the fine-root mass, particularly during the 2005 drought. Litterfall correlation with rainfall of sandy-loam terra-firme forest was time lagged as well as fine-root mass of the loamy-sand forest. The correlation between mortality and rainfall was weak, except for the loamy-sand forest (white-sand forest, 77%). High mortality rates occurred in the non-flooded forests for the censuses that included the dry years (2004–2005, 2005–2006). Interestingly, litterfall, AGB increment, and recruitment showed high correlation among forests, particularly within the loam-soil forest group. Nonetheless, leaf area index (LAI) measured in the most contrasting forests (clay and loamy-sand soil) was poorly correlated with rainfall, but highly correlated among them, which could be indicating a phenotypic response to the incident radiation in these sites; also, LAI did not reflect the differences in NPP components and their response to rainfall. Overall, the different temporal behavior of NPP components among forests in relation to rainfall fluctuations suggests the important role that soil exerts on the responses of plant species in each site, besides their effect on forest dynamics and community composition.