In a multi-scale approach to the study of the organic and mineral components in an active barrage-type tufa system of southern Italy, neo-formed deposits, in both natural depositional sites and on inorganic substrates placed in the stream for this study, were observed and compared through one year of monitoring. Dams and lobes representing the basic morpho-facies of the deposits are composed of two depositional facies: vacuolar tufa (a mixture of phytoclastic and framestone tufa) and stromatolitic tufa (phytoherm boundstone tufa). Three petrographic components comprise both facies: micrite and microsparite, often forming peloidal to aphanitc, laminar and dendrolitic fabrics, and sparite, which occurs as isolated to coalescent fan-shaped crystals forming botryoids or continuous crusts. All fabrics occurring in all depositional facies are organized into layers with a more or less well-developed cyclicity, which has its best expression in stromatolitic lamination. The precipitation of all types of calcite (with Mg 1·0 to 3·2 mole % and Sr 0·5 to 0·8 mole %) takes place more or less constantly during all seasons, in spite of the low saturation state of the water (the saturation index range is 0·75 to 0·89) within the active depositional zone; the latter extends for a few hundred microns through the external surface of the deposit. The active depositional zone has a particular micro-morphology composed of porous micro-columns (50 to 150 μm in size), separated by interstitial channels. Mineral precipitation occurs upon both external surfaces and within internal cavities of the micro-columns, while further point sites of precipitation occur suspended within the masses of cyanobacterial tufts. Sub-spherical mineral units, ‘nano-spheres’ (10 to 20 nm in diameter) are the basic biotic neo-precipitate; they commonly form by replacing non-living degrading organic matter and at point sites along the external surface of living cyanobacterial sheaths. Nano-spheres agglutinate to form first rod-shaped aggregates (100 to 200 nm) which then evolve into triads of fibres or polyhedral structures. Successively, both triads and polyhedral solids coalesce to form larger calcite crystals (mainly tetrahedrons tens of microns in size) that represent the fundamental bricks for the construction of the micro-columns in the active depositional zone. Precipitation is attributed to the presence of a widespread biofilm that occurs in the active depositional zone; this is composed of a heterogeneous community comprising epilithic and endolithic filamentous cyanobacteria, green algae, unicellular prokaryotes, actinobacteria and fungi, with a variable amount of extracellular polymeric substances. No precipitation takes place where the biofilm is absent, indicating that the biological activities of the biofilm are crucial, with its living organisms and non-living organic matter. Basic aggregates of neo-precipitates do not form in association with any one particular type of organic matter substrate, but appear to be related to the seasonal temperature variation: polyhedral micro-crystals mainly precipitate in the colder season, short triads in the intermediate seasons, and long triads in the warmest conditions. These three basic crystal aggregates have a petrographic counterpart, respectively, in the spar, microspar and micrite.