Geomicrobiological analysis of calcifying biofilms of three alkaline salt lakes characterized by moderate to high carbonate alkalinity indicates that microbial carbonate rock formation is not directly linked to cyanobacterial carbon fixation. The present review summarizes results from two published case studies that have been carried out at Pyramid Lake, USA, and Lake Nuoertu, PR China. New observations and data are presented for a current project on Satonda Crater Lake, Indonesia, that revise previous conclusions concerning the relationship between cyanobacteria and biofilm calcification. Extracellular polymeric substances (EPS) in the investigated lakes are mostly produced by cyanobacteria; their properties are discussed as key factors in biofilm calcification. In particular, EPS are capable of binding divalent cations (e.g. Ca2+) from the liquid phase by their carboxylate and sulphate groups. Therefore, despite a high supersaturation of the lake water with respect to calcium carbonate minerals, precipitation does not take place immediately. A delayed onset of precipitation can be achieved by a continuous Ca2+ supply that exceeds the Ca2+-binding capacity of the EPS, and/or an exoenzymatic degradation (decarboxylation, cleavage) of mucous substances that reduces the binding capacity and causes secondary Ca2+ release. The resulting microcrystalline precipitates are randomly distributed within the EPS, usually away from any of the living cyanobacteria. This suggests that the effect of photosynthetic CO2 fixation in increasing supersaturation is of secondary importance at high alkalinities. In contrast to biofilm-covered surfaces, calcium carbonate minerals nucleate and grow rapidly at surfaces poor in EPS when the critical supersaturation level for non-enzymatically controlled carbonate precipitation is reached. Examples of such surfaces poor in EPS are dead, lysed green algal cells and thin, discontinuous biofilms in voids of microbial reef rocks. Calcium carbonate crystals directly linked to cyanobacterial cells or filaments have been observed only exceptionally, e.g. on Calothrix.