Large-scale human activities including the extensive combustion of fossil fuels have caused acidification of freshwater systems on a continental scale, resulting in reduced species diversity and, in some instances, impaired ecological functioning. In regions where acidity is natural, however, species diversity and functioning seem to be less affected. This contrasting response is likely to have more than one explanation including the possibility of adaptation in organisms exposed to natural acidity over evolutionary time scales and differential toxicity due to dissimilarities in water chemistry other than pH. However, empirical evidence supporting these hypotheses is equivocal. Partly, this is because previous research has mainly been conducted at relatively small geographical scales, and information on ecological functioning in this context is generally scarce. Our goal was to test whether anthropogenic acidity has stronger negative effects on species diversity and ecological functioning than natural acidity. Using a meta-analytic approach based on 60 datasets, we show that macroinvertebrate species richness and the decomposition of leaf litter -- an important process in small streams -- tend to decrease with increasing acidity across regions and across both the acidity categories. Macroinvertebrate species richness, however, declines three times more rapidly with increasing acidity where it is anthropogenic than where it is natural, in agreement with the adaptation hypothesis and the hypothesis of differences in water chemistry. By contrast, the loss in ecological functioning differs little between the categories, probably because increases in the biomass of taxa remaining at low pH compensate for losses in functionality that would otherwise accompany losses of taxa from acidic systems. This example from freshwater acidification illustrates how natural and anthropogenic stressors can differ markedly in their effects on species diversity and one aspect of ecological functioning.