Conditions for the preservation of recent aragonite-rich sediments during early diagenesis in two semi-enclosed Mediterranean karstic seawater lakes on the island of Mljet (Adriatic Sea) were examined. The concentrations and stable isotope compositions of carbonate and sedimentary organic matter, as well as the geochemical parameters in pore water were measured. It was found that the smaller lake (Malo Jezero) receives considerably more terrestrial detritus than the larger lake (Veliko Jezero). A decrease in carbonate δ¹³C values with depth indicated a rather intensive transfer of organically derived C into the carbonate pool by diagenetic recrystallisation, masking the changes in carbonate δ¹³C caused by increasing amounts of aragonite. Dissolution of calcite as a result of CO₂ released from the decomposition of organic debris and the upward diffusive flux of dissolved inorganic carbon were together responsible for up to 24% of the dissolved inorganic carbon added to the pore water. This indicated locally occurring carbonate dissolution, irrespective of its saturation state in the bulk sediment. Despite the larger input of terrigenous material into Malo Jezero, the carbonate content in the sediment was much higher than in Veliko Jezero, indicating greater authigenic aragonite production. As magnesium calcite accounted for most of the carbonate dissolution, aragonite preservation in the sediment is favoured.