This study investigated ecological factors affecting species distribution and travertine deposition in an Italian site of the "Natura 2000" network. Vegetation plots were located along four streams in a prealpine valley (Valganna, Lombardy, Northern Italy). Five meso-scale variables (e.g. altitude, aspect and slope) and ten micro-scale variables (e.g. shading, plot position and soil accumulation) were recorded for each plot; in addition, travertine deposition was evaluated. The main floristic gradients extracted by DCA were related to topography, vegetation type and water availability. The occurrence of species groups in relation to environmental variables was analysed using Poisson regression. Amongst 15 environmental variables and six species, the variables showing the greatest relationship to travertine deposition were the length of the waterless period and substrate slope. Photosynthetic organisms had a minor role in travertine formation, mostly restricted to substrates with a shallow slope. The maintenance of a sufficient water flow is the most effective action in conservation plans for petrifying springs. © Birkhäuser Verlag, Basel/Switzerland 2009.