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Aim The highly endemic fishes of the arid Southwest USA have been heavily impacted by human activities resulting in one of the most threatened fish faunas in the world. The aim of this study was to examine the patterns and drivers of taxonomic and functional beta diversity of freshwater fish in the Lower Colorado River Basin across the 20th century.

Location Lower Colorado River Basin (LCRB).

Methods The taxonomic and functional similarities of watersheds were quantified to identify patterns of biotic homogenization or differentiation over the period 1900-1999. Path analysis was used to identify the relative influence of dam density, urban land use, precipitation regimes and non-native species richness on observed changes in fish faunal composition.

Results The fish fauna of the LCRB has become increasingly homogenized, both taxonomically (1.1% based on beta(sim) index) and functionally (6.2% based on Bray-Curtis index), over the 20th century. The rate of homogenization varied substantially; range declines of native species initially caused taxonomic differentiation (-7.9% in the 1960s), followed by marginal homogenization (observed in the 1990s) in response to an influx of non-native species introductions. By contrast, functional homogenization of the basin was evident considerably earlier (in the 1950s) because of the widespread introduction of non-native species sharing similar suites of biological traits. Path analysis revealed that both taxonomic and functional homogenization were positively related to the direct and indirect (facilitation by dams and urbanization) effects of non-native species richness.

Main conclusions Our study simultaneously examines rates of change in multiple dimensions of the homogenization process. For the endemic fish fauna of the LCRB, we found that the processes of taxonomic and functional homogenization are highly dynamic over time, varying both in terms of the magnitude and rate of change over the 20th century.