Global change is increasing biotic homogenisation globally, which modifies the functioning of ecosystems. While tendencies towards taxonomic homogenisation in biological communities have been extensively studied, functional homogenisation remains an understudied facet of biodiversity. Here, we tested four hypotheses related to long‐term changes (1991 ‐ 2016) in the taxonomic and functional arrangement of freshwater macroinvertebrate assemblages across space and possible drivers of these changes. Using data collected annually at 64 river sites in mainland New Zealand, we related temporal changes in taxonomic and functional spatial β‐diversity, and the contribution of individual sites to β‐diversity, to a set of global, regional, catchment and reach‐scale environmental descriptors.

We observed long‐term, mostly climate induced, temporal trends towards taxonomic homogenisation but functional differentiation among macroinvertebrate assemblages. These changes were mainly driven by replacements of species and functional traits among assemblages, rather than nested species loss. In addition, there was no difference between the mean rate of change in the taxonomic and functional facets of β‐diversity.

Climatic processes governed overall population and community changes in these freshwater ecosystems, but were amplified by multiple anthropogenic, topographic, and biotic drivers of environmental change, acting widely across the landscape. The functional diversification of communities could potentially provide communities with greater stability, resistance, and resilience capacity to environmental change, despite ongoing taxonomic homogenisation. Therefore, our study highlights a need to further understand temporal trajectories in both taxonomic and functional components of species communities, which could enable a clearer picture of how biodiversity and ecosystems will respond to future global changes.