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In the 1960s and 1970s, acidification was identified as a major environmental problem in Scandinavia, Great Britain and North America. In Sweden, a liming program was launched in order to counteract the effects of acidification on surface waters. More than 30 years after large-scale liming began, there is still debate about whether liming actually achieves its goals, i.e., to prevent acidification in acid-sensitive surface waters and to restore natural conditions in acidified waters. We used Detrended Correspondence Analysis (DCA) and analogue matching of diatom assemblages in surface sediment samples (recent conditions) from 31 limed lakes and pre-industrial samples from 291 reference lakes to help answer the question as to whether the Swedish liming program achieves its goals. Diatoms are important primary producers in lakes and established indicator organisms for lake-water quality. First we compared pre-industrial with post-limed diatom communities to address the question whether liming causes unnatural conditions, i.e., diatom communities that have not previously occurred in Swedish lakes. Second, we addressed the issue of what is a realistic condition to use as a reference (natural condition) or a target in management programs. We found that the diatom communities in limed lakes were not different from the communities in the reference lakes. Most of the limed lakes had one or more analogues within the reference data set and many of them had at least one within-lake analogue. Hence, liming does not create unique diatom communities in lakes. Based on this and previous paleolimnological studies in Swedish lakes we suggest a conceptual model integrating the natural lake condition, the historical human impact, and the recent and contemporary human impact, when defining realistic targets in management programs.