Here, we employ an additive partitioning framework to disentangle the contribution of spatial turnover and nestedness to beta diversity patterns in the global freshwater fish fauna. We find that spatial turnover and nestedness differ geographically in their contribution to freshwater fish beta diversity, a pattern that results from contrasting influences of Quaternary climate changes. Differences in fish faunas characterized by nestedness are greater in drainage basins that experienced larger amplitudes of Quaternary climate oscillations. Conversely, higher levels of spatial turnover are found in historically unglaciated drainage basins with high topographic relief, these having experienced greater Quaternary climate stability. Such an historical climate signature is not clearly detected when considering the overall level of beta diversity. Quantifying the relative roles of historical and ecological factors in explaining present-day patterns of beta diversity hence requires considering the different processes generating these patterns and not solely the overall level of beta diversity.

Aim  To identify key research questions and challenges that will, if addressed in a timely manner, significantly advance the field of freshwater fish biogeography and conservation. Location  Globe. Methods  By drawing on expertise from different regions of the world, we integrate an illustrative conspectus of recent scientific advancements in fish biogeography with a prospectus of needed areas of scientific inquiry to identify information gaps and priority research needs to advance the science. Results  We identified the following core challenges: (1) Testing current and forging new theories in biogeography; (2) Advancing a trait‐based biogeography of freshwater fishes; (3) Quantifying extinction risk and loss of fish species in a changing environment; (4) Evaluating the magnitude and geography of extinction debt for freshwater fishes; (5) Elucidating the patterns and drivers of freshwater fish invasions; (6) Forecasting the future geography of freshwater fishes; (7) Understanding the interactive effects of multiple stressors in freshwater ecosystems; (8) Quantifying new features of the biodiversity crisis: fish faunal homogenization and the emergence of novel assemblages; (9) Promoting scientific rigour in emerging freshwater fish conservation strategies and (10) Improving conservation planning strategies for freshwater fish species. Main conclusions  By reflecting on recent scientific progress in fish conservation biogeography, we have identified a set of core challenges and priorities requiring future research investment.