Carbonate precipitates in biofilm were investigated from hot springs near Viterbo, Italy; Salt Pond, San Salvador; and Fowl Cay Reef, Abaco, Bahamas. Features shared by hot springs and salt ponds are supersaturation with CaCO3, abundant Spirulina, and clustered acicular aragonite crystals termed “fuzzy dumbbells.” TEM and FESEM microscopy show fuzzy dumbbells contain a core of amorphous organic matter and subhedral CaCO3 microcrystals arranged in linear fabrics. Micron- to millimeter-scale microenvironments are identified by localized dissolution, the occurrence of gothic calcite inter-grown with organic filaments, and the presence of calcite in biofilm where aragonite is chemically favored. Spherical CaCO3 precipitates in reefs were anticipated, but not encountered in TEM sections of reef biofilm. In conclusion, biofilm creates the microenvironment and organic matter provides substrate for fuzzy dumbbell precipitation. TEM is a novel technique for studying the relationship between organic matter and CaCO3 precipitation, and has potential medical, industrial, and academic applications.