A series of experiments on freshwater carbonates (tufas) involving biofilm colonization in both fast-flow and slow-flow mesocosms was carried out in order to assess the changing nature of biofilm and associated precipitates under contrasting conditions. A thin biofilm developed over 14 weeks during the 'summer' experimental run contained a basal calcite layer overlain by small calcite crystals suspended within the Extracellular Polymeric Substances (EPS). The 'autumn' biofilm, however, showed the development of multi-laminated calcite precipitates within the EPS despite constant environmental conditions throughout the run. The experiments also showed that the largest volume of calcite precipitate developed in the fast-flow flumes regardless of temperature control. Development of an extensive calcite layer at the base of EPS in conditions of complete darkness within the sump was also observed. This study provides increased weight for the concepts: (1) that fresh-and saltwater stromatolites appear to be highly comparable multi-laminated systems with precipitation strongly influenced by both phototrophic and heterotrophic microbes; and (2) that microbial precipitation may be more common within aphotic (including cave, lake bottom and soil) systems than has previously been considered.