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ABSTRACT Aim Assess how local variations in bird taxon composition across lowland Amazonia are associated with environmental factors and rivers. Location Lowland Amazonia below 500 m a.s.l., South America. Time Period Contemporary. Major Taxa Studied Birds. Methods We constructed maps illustrating changes in bird taxon composition across lowland Amazonia and calculated Jaccard dissimilarity between adjacent localities. We then applied geographically weighted regression (GWR) to evaluate how variation in environmental variables and riverine features (width, water discharge, meandering, floodplain extent) explains spatial turnovers in taxon composition. We used comparative phylogenetic analyses to test whether ecological traits predict cross‐river taxon turnover. Results Geographic variation in bird taxon composition was mostly associated with the presence and physical characteristics of rivers, especially river width and discharge, which predicted composition dissimilarities along their lower courses. Away from rivers, variations in forest cover, habitat heterogeneity, and temperature seasonality were the strongest variables associated with composition turnovers. Phylogenetic analyses showed that taxa inhabiting terra firme forests were disproportionately likely to exhibit cross‐river replacements, whereas dispersal‐related morphological traits had limited explanatory power. Main Conclusions Local Amazonian bird taxon composition is primarily associated with variation in forest cover, habitat heterogeneity, and temperature seasonality, except across major rivers. The influence of river characteristics, particularly width and discharge, on bird taxon turnover highlights the role of rivers in structuring Amazonian biodiversity at local and global scales. Because these variables operate at different scales, taxon composition turnover patterns reflect a mosaic of ecological and geomorphological processes. These findings highlight the need for conservation strategies that account for bird habitat specialisation, river dynamics, and ongoing landscape changes.