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Abstract Aim Freshwater biodiversity is declining world‐wide as a result of human‐caused degradation of freshwater ecosystems. Declines in species richness are well documented for many taxonomic groups, but less is known about how and why species composition and beta diversity (β) change in response to environmental degradation in freshwater environments. Location The Mid‐ A tlantic Highlands region of the USA (36–42° N , 74–82° E ) and F inland in northern E urope (60–68° N , 20–32° E ). Methods We used null models, occupancy analyses, ordinations and multitaxon niche models to assess how β of stream macroinvertebrate assemblages in two biogeographically distinct regions responded to environmental alteration and what mechanisms were most likely to have caused the observed differences in β. Results Macroinvertebrate assemblages at anthropogenically disturbed sites were significantly more dissimilar from one another than were reference sites, a result contrary to those reported in several other studies. In this study, anthropogenic disturbances decreased the regional prevalence of most common taxa and increased the prevalence of several less common taxa. These differences in taxon occupancies and β between the reference condition and disturbed streams are unlikely to be the result of a single mechanism, although environmental filtering was probably of primary importance. Main conclusions The effects of anthropogenic disturbance on assemblage composition can be variable and probably depend on: initial ecological conditions; the magnitude, type and uniformity of environmental alteration occurring in a region; and the sensitivity of individual taxa. It is unlikely that β is controlled by a single mechanism, and these variable mechanisms may have diverse effects on taxon occupancies and hence β. Restoration ecologists will need to consider how β varies naturally across different landscape settings and in response to different types of disturbance when developing region‐wide restoration strategies.