Fishes of the Western Amazon exhibit the greatest diversity of any continental vertebrate fauna on Earth. Hypotheses to explain diversity patterns have focused on various ecological and evolutionary processes, yet we have historically lacked detailed knowledge of species’ geographic distributions and habitat tolerances to test these alternative hypotheses. We compare spatial patterns in newly-compiled high-resolution fish distributions from the Colombian Amazon with those of eight geomorphologically-defined ecosystems: Andean rivers and streams, foothill alluvial rivers, major low-gradient rivers, lowland rapids, lowland floodplains, lowland small rivers and “terra firme” streams, and high-gradient shield streams. An incidence matrix containing 905 native species, based on ~16,000 museum records, was subjected to multivariate analyses (hierarchical clustering on principal components and PERMANOVA) to assess the association between species composition and geomorphology. We used variation partitioning and differences in species composition due to adjacency between ecosystems to determine spatial autocorrelation. We followed a network approach to identify ecological specializations. Our analysis found evidence of spatial autocorrelation, supports two major species assemblages in Andean and lowland settings, and four major habitat clusters: Andean systems (rivers, streams, and foothills), lowland systems (major rivers, floodplains, and small rivers and streams), rapids, and shield streams. Network analysis detected significant modularity, indicating species geomorphological specialization. We provide the first study of fish distributions in the Western Amazon using geomorphologically-defined habitat categories, finding that local fish assemblages are not randomly selected from the regional fauna. Instead, species show significant habitat specialization according to geomorphology, which might act as an environmental filter according to species phenotype. Composition of freshwater fish assemblages from the Western Amazon supports the hypothesis that species follow deterministic assembly rules. Geomorphologically-defined ecosystems might act as an environmental filter selecting species from the regional pool according to their phenotype. Fish assemblages describe non-random spatial distribution, where closer geomorphologically-defined ecosystems tend to be more similar. We provide the first general ecological perspective of fish distributions in the Western Amazon based on quantitative analyses. This study also identifies aquatic ecosystems - largely determined by geomorphology - to be treated as units for conservation to mitigate diversity loss.