Predictive Digital Soil Mapping (PDSM) in Eastern Amazonia faces challenges due to its environmental complexity, difficult access, and scarce legacy data. While legacy soil maps contain valuable tacit knowledge, updating them requires methods that can handle uncertainty. This study evaluates the integration of old soil maps with machine learning to update soil information in Tracuateua, Pará, with a specific focus on the performance of ensemble learning and the explicit incorporation of uncertainty metrics in soil mapping units under hydromorphic influence, which, in addition to being difficult to access, are influenced by complex pedogenetic processes. We combined 270 sampling points, equivalent to the total pixels that captured the variability of soil mapping units, with environmental covariates and historical data. Several algorithms were tested, including an ensemble approach, to predict mapping units and quantify uncertainty through entropy and confusion indices. The ensemble model demonstrated improved stability and reduced classification uncertainty compared to single models, particularly in challenging hydromorphic environments. Although accuracy gains were modest, the models captured soil–environment relationships, with climate as: Annual Mean Temperature 22,000 years ago (Tmean_22k), relief: Channel Network Base Level (CNBL and altitude) and organism variables: Land Surface Temperature (LST) emerging as the main predictors. Spatialized uncertainty estimates, expressed through entropy and the confusion index, provide a practical decision-support tool for guiding field surveys and identifying areas of low mapping reliability. By explicitly transferring the pedologist’s mental model—encoded as tacit knowledge in legacy soil maps—into ensemble learning, this study presents a robust and transferable framework for updating soil maps in data-scarce tropical regions, balancing predictive performance, spatial consistency, and uncertainty-aware interpretation.