Acidification has led to a strong decline of species characteristic of shallow soft-water lakes. In spite of reductions in acidifying deposition, natural recovery of biodiversity is modest or even absent, suggesting that the impact of acidification is difficult to reverse. We compared recovery from acidification in non-restored and restored lakes using data from 1983 and 2004. In restored lakes, accumulated organic matter was removed and alkaline water was supplied, resulting in an increase in pH and alkalinity and a decrease in ammonium, sulphur and aluminium. For evaluation of biotic changes we selected chironomid larvae (Diptera). In restored lakes, rarefied species richness increased, chironomid species composition changed and responses of chironomid taxa and their life-history strategies indicated a shift towards pre-acidification assemblages. Species adapted to dynamic and stressful environments decreased in favour of those with life history strategies suitable for more benign environments. In non-restored lakes, chironomid response did not indicate a recovery, despite an improved water chemistry in terms of decreased acidity and sulphur (not ammonium and aluminium). Instead, stressful conditions related to oxygen shortage became more prevalent as a decrease was observed in the chironomids least adapted to periods with low oxygen availability. Acidification has inhibited decomposition, resulting in the accumulation of organic material. Natural recovery from acidification resumed and increased the decomposition of this accumulated organic material, resulting in release of nutrients, consumption of oxygen and a decline of sensitive bottom-dwelling fauna such as chironomids. Therefore, active restoration by removal of accumulated organic matter from sand bottoms is essential for a recovery of chironomid assemblages.