The cyanobacterium Rivularia haematites has calcified to form unusually large (up to 10 m high) bioherms in the Pleistocene Gulf of Corinth. Today R. haematites calcifies only in freshwater environments but these Gulf of Corinth bioherms have a brackish affinity, limited areal extent, and occur within marine deposits. Field relations and preliminary U-series dating suggest a marine isotope stage (MIS) 5e age for the bioherms. This age is compatible with published MIS 5e ages for corals in the marine sediments above the bioherms and is consistent with their current elevation based on average uplift rates. Bioherm growth during MIS 5e constrains their formation during a time of near sea-level highstand when the Gulf of Corinth was marine. Growth cavities in the bioherms are encrusted by brackish tolerant coralline algae. Field mapping of the MIS 5e highstand palaeoshoreline shows the bioherms grew in water <16 m deep. Mg contents of the bioherm calcites, and associated coralline algal skeletons, are both much lower than expected for marine MIS 5e carbonates. They are best explained if the calcites precipitated from brackish fluids with Mg/Ca ratios below 2, implying at least 60% input of freshwater with low Mg/Ca ratio. Sr isotopes confirm a strong input of groundwater that had partially equilibrated with Mesozoic limestones. The limited areal extent of the bioherms and their close association with karstified fault scarps suggest that they formed in shallow sea water where freshwater submarine springs delivered CaCO3 saturated water that promoted rapid calcification of cyanobacteria. Rapid calcification and strong degassing of CO2 from the spring water resulted in disequilibrium stable isotope compositions for the calcites.