Two branches forming the headwaters of a stream in the Czech Republic were studied. Both streams have similar catchment characteristics and historical deposition; however one is rain-fed and strongly affected by acid atmospheric deposition, the other spring-fed and only moderately acidified. The MAGIC model was used to reconstruct past stream water and soil chemistry of the rain-fed branch, and predict future recovery up to 2050 under current proposed emissions levels. A future increase in air temperature calculated by a regional climate model was then used to derive climate-related scenarios to test possible factors affecting chemical recovery up to 2100. Macroinvertebrates were sampled from both branches, and differences in stream chemistry were reflected in the community structures. According to modelled forecasts, recovery of the rain-fed branch will be gradual and limited, and continued high levels of sulphate release from the soils will continue to dominate stream water chemistry, while scenarios related to a predicted increase in temperature will have little impact. The likelihood of colonization of species from the spring-fed branch was evaluated considering the predicted extent of chemical recovery. The results suggest that the possibility of colonization of species from the spring-fed branch to the rain-fed will be limited to only the acid-tolerant stonefly, caddisfly and dipteran taxa in the modelled period.