Diatoms are considered unicellular eukaryotic organisms exclusively depositing biogenic silica. Heretofore there has been no report of calcification by these algae. Here it is shown that calcium carbonate within the stalks of Didymosphenia geminata, a nuisance species that has prolifically colonized streams and rivers globally, is biogenic in origin and occurs as a network of calcite nanofibers. The nanofibrous framework in the mineralized polysaccharide matrix imparts mechanical support to the stalks, providing stability in variable flow conditions. The results demonstrate that D. geminata possesses cellular and periplasmic carbonic‐anhydrases that contribute to carbon fixation and biomineralization, respectively. The activity of external carbonic‐anhydrase was more than 50% of the total activity, which points to its role in anchoring this bioeroding diatom on hard surfaces. The first evidence of multiphase biomineralization by diatoms that deposit both biogenic silica and crystalline biogenic calcite which are imparting distinct functional advantage to the organism is provided.