Studies investigating changes in community composition in response to recent climate warming are mostly restricted to one-dimensional (e.g. latitudinal) gradients, whereas species movements are in reality three dimensional. Based on 3,245 benthic invertebrate samples from Central European streams over large altitudinal, latitudinal and longitudinal gradients, and covering the period 1986-2009, we have developed an advanced community temperature index (CTI). This CTI enables the analysis of three-dimensional community range shifts not only in freshwater but also in marine and terrestrial environments. Overall, and in contrast to terrestrial species, benthic invertebrate communities have been able to keep up with recent climate warming. However, their ability to track temperature shifts differed grossly between the three spatial dimensions, with the strongest response to elevation. Nevertheless, the price these communities had to pay was high, as total benthic invertebrate abundance and richness in low-temperature dwelling species have already declined by 21% and 52.5%, respectively. Our approach has emphasized the complex reaction of species towards increasing temperatures, allowing a more complete picture of the subtle community shifts in response to climate change.