AbstractThis study collated information relating to acidification of running and standing waters on Sites of Special Scientific Interest (SSSIs) throughout Britain in acid‐sensitive areas.Of those SSSIs which occur in acid‐sensitive areas of Britain, 196 have water bodies. The following information was obtained for each site if available: details of local geology and soils, types of land use and management, water quality data and data relating to biological components of both the aquatic and riparian habitats.In addition, samples from 112 water bodies were collected for water chemistry and epilithic diatom analysis. Results from each site were placed into existing critical loads and species response models to determine whether acidification had occurred.Results showed that the fresh waters on 141 SSSIs had probably suffered acidification. This was most acute in north Wales, with mid Wales, south‐west and north‐east Scotland and northern England also being badly affected.A wide variety of changes in the biological status of water bodies relating to acidification were found to have been recorded on SSSIs, ranging from phytoplankton, invertebrate and macrophyte community changes to decline of fish, amphibian, bird and mammal populations.Catchment afforestation may be a problem in poorly buffered areas and has probably contributed to freshwater acidification on 40 SSSIs.Comparison with critical loads maps for acidity in UK fresh waters reveals that existing commitments on acidifying emissions (the EC Large Combustion Plant Directive) will not be sufficient to prevent further acidification on a number of SSSIs. In order to achieve a protection of the nature conservation interest of fresh waters further commitments to emission reductions will be ne