Acidification has strongly affected natural ecosystems due to the deposition of acidifying pollutants in geographical areas with low buffering capacity. Here we show both that taxonomic richness of benthic invertebrates (as a measure of stream health) and breakdown rate of leaf litter (a major process in stream ecosystems) in three naturally acid streams were not significantly different from richness and breakdown rates of three circumneutral control streams in the same area in northern Sweden. In contrast, a comparative data-set representing a gradient from circumneutral to acidified streams in France showed decreasing richness and litter breakdown rates (by 60% and 70% between pH 6.5 and 4.5, respectively) typical of acidified streams. The strong negative effects found in many freshwater systems may be a consequence of low capacity to adjust to rapidly changed conditions. In contrast, organisms in naturally acidic systems, such as streams of the boreal region in catchments with accumulating organic material and a geology poor in buffering substances, seem better adapted as a consequence of protracted exposure to low pH over evolutionary time. These results have implications for the management of streams and rivers in northern Sweden, where considerable efforts are spent on remediation without consideration of the fact that the natural state of many of these systems is acidic.