Stable isotope and geochemical data are used here to differentiate between contemporaneous abiotic and microbial processes leading to formation of modern carbonate- (calcite, aragonite and magnesite) and silicate-rich (kerolite) mineralization in basaltic sea caves on the island of Kauai, Hawaii. Strontium isotope and Ca/Sr ratios in meteoric water and cave carbonates suggest that the majority of Sr and Ca are derived from rock–water interaction within the host basalts situated above the caves. Oxygen and hydrogen isotope ratios and chemical compositions of cave and surface waters indicate that evaporation does not control cave-water composition. However, evaporation of drops and thin films of water in microenvironments can lead to precipitation of some phases. This behaviour is suggested by the covariance in δ18O and δ13C values of some carbonates, especially magnesite, which is considered to be a late-stage evaporative precipitate. Modelling of water evolution suggests that evaporation can be a cause of supersaturation for magnesite, kerolite and some Ca carbonates. However, the highly elevated δ13C values (up to +8.2) of some Ca carbonates, compared to average dissolved inorganic carbon δ13C values (~−12), are best explained as the product of microbial photosynthesis, in particular by cyanobacteria, present in the upper layers of active microbial mats on cave surfaces. The preferential uptake of 12C by cyanobacteria is recorded in the low δ13C values (−29.1 to −22.6) of organic matter in mats and mineralized microbialites. The resulting 13C-enrichment of dissolved inorganic carbon is recorded in the elevated δ13C values of these Ca carbonates. A positive correlation exists between the δ13C values of the carbonates and coexisting organic matter. The large enrichment in 13C of carbonate minerals, relative to dissolved inorganic carbon, and its covariance with the δ13C values of coexisting organic matter are useful for identification of carbonate-rich mineralization resulting from autotrophic microbial activity.