Rivers are among the world's most modified ecosystems, with poor water quality representing a prominent problem for over 200 years, especially in urban areas. In Western Europe, however, industrial decline, tighter regulation and improved wastewater treatment have combined over recent decades to create conditions conducive to extensive restoration and positive biological change. Here, we evaluate the river macroinvertebrate fauna of England and Wales in relation to water quality, physical habitat and climate over almost two decades. We predicted that biological recovery would be characterized by: (i) greater taxon richness and prevalence of pollution-sensitive taxa, (ii) larger changes in more heavily urbanized catchments, and (iii) temporal trends in assemblage structure that correlated with improving water quality. Family level richness increased on average by nearly 20% during 1991–2008, accompanied by a widespread shift towards taxa characteristic of well-oxygenated and less polluted waters. Changes were largest in the most urbanized catchments. A combination of natural gradients and anthropogenic pressures explained the variation among sites, whereas temporal changes correlated with improving water quality and variations in discharge. Positive trends were not universal, however, and there was localized deterioration in some streams draining upland areas and in the lowland south east. Our results are consistent with a large-scale ecological recovery of English and Welsh rivers since 1990, probably continuing a trend from the mid-20th century. Based on these results, we suggest: (i) freshwater communities are resilient to long-term anthropogenic pressures, (ii) biodiversity benefits can arise from investment and long-term restoration intended largely to enhance ecosystem services such as drinking water and sanitary concerns, and (iii) long-term monitoring data collected for statutory purposes–based in this case on nearly 50 000 samples–can address scientific questions at spatial and temporal extents seldom achieved in research programmes.