Regional and local processes are thought to influence community phylogenetic and species diversity, but have proved challenging to distinguish. We disentangled the effects of local (limiting similarity and habitat filtering) and regional processes (biogeography, history and geographical constraints) on the species and phylogenetic diversity of native riverine fish communities across France. Fish species richness (SR), phylogenetic diversity (estimated as the phylogenetic species variability metric, PSV) and trait evenness (estimated from 17 ecological and life-history traits) were estimated for fish at 932 sampling sites across 42 river basins in France. A phylogenetic signal in traits and species responses to environment variation were estimated using linear models. Null models were developed to test whether river basins constrain the PSV of the communities. Hierarchical linear models were fitted to PSV and SR to partition the variance explained by local and regional processes. Fish species richness and phylogenetic diversity were negatively correlated across sites (r = -0.589, P < 0 001). There was a phylogenetic signal in species traits, but only a weak signal in species responses to environmental variation across sites. The null models suggested that river basins constrain community PSV. Local-scale predictors (temperature, landscape position and trait evenness) explained the variation in both PSV and SR, while regional-scale predictors (latitude, longitude and basin surface area) explained the variation only in SR. Significant interaction terms between local- and regional-scale predictors were also detected for both metrics. Local-scale processes, habitat filtering and limiting similarity, probably determine the species composition of fish communities across France, while broad-scale, regional processes constrain community composition both directly and indirectly by affecting the strength of these local-scale processes. By analysing phylogenetic diversity and species richness simultaneously, a full picture of the drivers of local-scale diversity can be determined. © 2013 John Wiley & Sons Ltd.