The role of cyanobacterial communities in the formation of carbonate sediments (an-cient and modern) is not completely clear. We studied the cyanobacterial communities connected with carbonate sediments of the freshwater bodies feeding the historical Peterhof fountains (Saint-Petersburg, Russia). Cyanobacterial communities were studied by metagenome analysis and optical microscopy. Carbonates associated with cyanobacterial communities (both in situ and in vitro) were studied by powder X-ray diffraction analysis, scanning electron microscopy, energy-dispersive X-ray spectroscopy, and Raman spectroscopy. The interconnection between the mineral composition of carbonate sediments and inhabiting microorganism species was established. The leading role of cyanobacteria in carbonate biomineralization in fresh water of Peterhof fountains water supply system was shown. Cyanobacteria of 24 genera were revealed in sediments composed of calcite and aragonite. The crystallization of carbonates on the surface of 13 species of cyanobacteria was found. Using model experiments, a significant contribution of cyanobacterial species of the Oscilla-toriaceae family (Phormidium spp., Lyngbya sp., Oscillatoria formosa) to carbonate biomineralization is demonstrated.