Macroinvertebrate communities in Western European rivers have changed substantially in recent decades. Understanding the causes is challenging because improvements in water quality have coincided with climatic variations over this period. Using data covering >2300 rivers and 21 years (1991–2011) across England and Wales, we analysed family-level distributions and nationwide trends in prevalence (proportion of sampling locations where an organism was present) to diagnose the causes of ecological change. Our aims were to: (i) reveal the taxa driving assemblage-level trends; (ii) identify the main changes in family-level prevalence and distribution patterns; and (iii) test whether changes were accounted for by improving water quality, increasing temperatures or variations in discharge. While previous analyses revealed increasing richness among British river invertebrates, a partial turnover of taxa is now evident. Two distinct components of temporal trend have comprised: (i) overall increases or decreases in taxon prevalence over 21 years, which correlated with pollution sensitivity and discharge; and (ii) short-term variations in prevalence that correlated primarily with temperature and nutrient concentrations. The longer-term changes in prevalence were reflected in expansions or contractions in families' distributions linked to water quality, with little evidence of shifts consistent with increasing temperatures. Although these monitoring data had limitations (e.g., family-level data, few headwaters), they provide no clear evidence of long-term climate effects on invertebrates; the one feature consistent with climate warming – a small northward expansion of the range of many taxa – was accounted for by large improvements in water quality in northern England. Nevertheless, changes linked to discharge and temperature over the shorter-term (<2 years) point to the climatic sensitivity of invertebrate communities. It is therefore likely that any long-term climatic changes since 1990 have been outweighed by the strength and geographical extent of the recovery from poor water quality.