Calcifying tufa stromatolites are forming on a high energy coast of the South African Indian Ocean. The tufa stromatolites form in upper intertidal to supra tidal rock pools, encrust bedrock and are linked both laterally and vertically to physico-chemical properties of their pool water. Calcification only occurs in pools where dissolved carbonate-rich, spring-fed groundwater is routed, and d18O values are consistent with calcification in a mixture of freshwater and seawater. Increasing pH and less negative isotope values away from the spring are consistent with CO2 degassing and in-stream calcification, albeit with some in-mixing of seawater. The rocky shore setting of these active tufa stromatolites is new and invites serious comparison with some Archaean rocky substrate peritidal stromatolites (e.g. the c. 3.45 Ga Strelley Pool sequences, Pilbara Craton). This new association shows that initial encrustation of rocky intertidal substrates can begin with freshwater influence in the intertidal zone, a facies detail that should be sought in ancient peritidal stromatolites.