AimContemporary dispersal constraints and environmental conditions are broadly recognized as significant drivers of beta diversity patterns. However, beta diversity patterns may also reflect the legacy of past climatic and geological events. In this study, we investigated the relative importance of historical and contemporary factors as drivers of taxonomic, functional and phylogenetic beta diversity in Neotropical stream communities.LocationThe Colombian Orinoco basin.TaxonDiatoms and insects.MethodsWe estimated taxonomic, phylogenetic and functional beta diversity using Baselga's (BAS) and Podani's (POD) frameworks. Following both frameworks, we further partitioned every biodiversity facet into turnover and nestedness or richness difference components. Then, we used generalized linear models (GLM) to relate each biodiversity facet with environmental, spatial and historical factors.ResultsWe found that both historical and contemporary factors affected current patterns of beta diversity. Historical factors and water pH and temperature had the strongest effect on beta diversity patterns, particularly for taxonomic and phylogenetic facets. GLM models performed better for insects than for diatoms in all three facets. Within communities, our analysis also revealed a partial congruence between BAS‐ and POD‐based results.Main conclusionsDue to their past geological history and contemporary environmental gradients, tropical montane streams are natural laboratories for disentangling the joint effects of ecological and biogeographical factors on biodiversity patterns. Our study reveals that present‐day distribution patterns cannot be fully explained without accounting for the effects of past geological and climatic events on mountain landscapes. In the Neotropics, montane geology sets the stage for speciation and landscape formation, with which ecological (e.g., dispersal limitation) and environmental factors interact to generate spatial variation in species turnover.