Freshwater ecosystems will be profoundly affected by global climate change, especially those in mountainous areas, which are known to be particularly vulnerable to warming temperatures. We modelled impacts of climate change on the distribution ranges of 38 species of benthic stream macroinvertebrates from nine macroinvertebrate orders covering all river zones from the headwaters to large river reaches. Species altitudinal shifts as well as range changes up to the year 2080 were simulated using the A2a and B2a Intergovernmental Panel on Climate Change climate‐warming scenarios. Presence‐only species distribution models were constructed for a stream network in Germany’s lower mountain ranges by means of consensus projections of four algorithms, as implemented in the BIOMOD package in R (GLM, GAM, GBM and ANN). Species were predicted to shift an average of 122 and 83 m up in altitude along the river continuum by the year 2080 under the A2a and B2a climate‐warming scenarios, respectively. No correlation between altitudinal shifts and mean annual air temperature of species’ occurrence could be detected. Depending on the climate‐warming scenario, most or all (97% for A2a and 100% for B2a) of the macroinvertebrate species investigated were predicted to survive under climate change in the study area. Ranges were predicted to contract for species that currently occur in streams with low annual mean air temperatures but expand for species that inhabit rivers where air temperatures are higher. Our models predict that novel climate conditions will reorganise species composition and community structure along the river continuum. Possible effects are discussed, including significant reductions in population size of headwater species, eventually leading to a loss of genetic diversity. A shift in river species composition is likely to enhance the establishment of non‐native macroinvertebrates in the lower reaches of the river continuum.