A new benthic freshwater diatom, Cymbella tridentina sp. nov., was identified with the aid of light and scanning electron micrographs. The most characteristic morphological features are the valve outline (in particular, the shape of the ventral margin), the number of stigmata, and the length/breadth ratio. The new species was epilithic in carbonate, mountain, flowing springs in 3 Natural Parks of the Alps. The environmental preferences of the new species, assessed by the comparative analysis of the sites where it was found and by seasonal and longitudinal-distribution data available for the type locality, are quite distinctive. The new species appears to be rheophilic and oligotraphentic (not present in N-enriched sites), characteristic of dolomite mountain ranges (even if dolomite is not the dominating carbonate rock in the basin), and to develop year-round with low relative abundances (peaks associated with high discharge in autumn and spring). The combination of these ecological requirements might determine the preferential occurrence of C. tridentina sp. nov. in close-to-pristine, carbonate, mountain, flowing springs. The preference of the new species for the spring zone of running waters, and its possible use as an integrity indicator, is discussed in the wider context of crenobiosis. The importance of oligotrophic headwaters for the integrity of running-water systems and for the conservation of freshwater biodiversity, is highlighted.