Surface water acidification was identified as a major environmental problem in the 1960s. Consequently, a liming program was launched in Sweden in the 1970s. The primary purpose of liming is to restore conditions that existed prior to acidification. To reach this goal, as well as achieve 'good status' (i.e. low levels of distortion resulting from human activity) in European freshwaters until 2016 under the European Union Water Framework Directive, lake data are required to define reference conditions. Here, we compare data from chemical/biological monitoring of 12 limed lakes with results of paleolimnological investigations, to address questions of reference conditions, acidification, and restoration by liming. Using diatom-based lake-water pH inferences, we found clear evidence of acidification in only five of the 12 lakes, which had all originally been classified as acidified according to monitoring data. After liming, measured and diatom-inferred pH agree well in seven lakes. The sediment record of three of the five remaining lakes gave ambiguous results, presumably due to sediment mixing or low sediment accumulation rates. It is difficult to determine whether liming restored the lakes to a good status, especially as some of the lakes were not acidified during the twentieth century. In addition to acid deposition, other factors, such as natural lake and catchment ontogeny or human impact through agricultural activity, influence lake acidity. This study shows that monitoring series are usually too short to define reference conditions for lakes, and that paleolimnological studies are useful to set appropriate goals for restoration and for evaluation of counter measures.