Despite international policy implementation to reduce atmospheric acid deposition and restore natural resources from cultural acidification, evidence of ecological recovery is equivocal. Failure to meet recovery goals means that acidification still threatens biodiversity in many areas of the world. Managers thus need information to manage biodiversity, especially its components that are sensitive to stress (acid-sensitive taxa). We analyzed 20-year time series (1988–2007) of water quality and littoral invertebrates in acidified and circum-neutral lakes across Sweden to evaluate regional biodiversity dynamics and the extent to which changes in water quality affect these dynamics. We used multivariate time series modeling to (1) test how individual species groups within invertebrate communities track changes in the abiotic environment and (2) reveal congruencies of taxon contributions to species group change across lakes. Chemical recovery in the lakes was equivocal, and increases of pH and alkalinity were observed in subsets of acidified and circum-neutral lakes. Time series analyses revealed two different patterns of species groups for invertebrate communities across lakes; the first species group showed monotonic change over time, while the second group showed fluctuating temporal patterns. These independent species groups correlated distinctly with different sets of environmental variables. Recovery of pH and alkalinity status was associated with species group patterns only in a few lakes, highlighting an overall weak recovery of invertebrate species. The sets of species, including acid-sensitive taxa, composing these species groups differed markedly across lakes, highlighting context-specific responses of invertebrates to environmental variation. These results are encouraging because disparate local-scale dynamics maintain the diversity of sensitive invertebrate species on a regional scale, despite persisting acidification problems. Our study can inform and help refine current acidification-related policy focused on sensitive biodiversity elements.