Holocene carbonate muds (<63- μm fraction) and macro-organic matter were collected from marine subtidal mudbanks and supralittoral mud islands of Florida Bay, and freshwater marshes of the Florida Everglades, U.S.A. Geochemistry, sedimentology and mineralogy were used to determine whether carbonate mud formation in specific marine and freshwater environments was geochemically distinct, and to assess the importance of early diagenetic reactions on mud chemistry and mineralogy. Significant variations were found in the relative amounts of carbonate minerals, not just between the marine and freshwater environments, but also within Florida Bay. In particular, Mg-calcite is enriched in Crane Key muds by ∼ 10%, relative to nearby Cross Bank. The Mg-calcite appears to precipitate in the surface-living cyanobacterial mats of the key, and seems to be linked to Mg chelation by the cyanobacterial organic matter. This Mg-calcite has a distinct δ 13C around − 4‰, ∼ 6‰ lighter than Mg-calcite derived from Thalassia epibionts in the Cross Bank muds. Dolomite was found just below the cyanobacterial mats, forming in the only part of the core where reactive organic carbon has been completely removed by sulphate-reducing bacteria. The δ 13C values of this dolomite (at least − 4‰) are consistent with previously published δ 13C values of dissolved inorganic carbon in pore waters at this horizon, which support dolomite formation in situ. Mg supply for dolomite formation may be from dissolution of the overlying cyanobacterial mat Mg-calcite. The various types of organic matter have distinctive δ 13C-values ranging from ∼ − 25‰ (mangrove and sawgrass) to ∼ − 10‰ (cyanobacterial mats) and − 8‰ ( Thalassia seagrass). Values intermediate between these end-members record mixing of the organic matter types, which shows particularly the time when the bank muds became dominated by Thalassia organic matter, i.e. were relatively removed from mangrove vegetation. Five Holocene mud suites (bank, key, cyanobacterial mats, mangrove swamp and freshwater Everglades swamp) show distinct chemical signatures in their mean δ 13C, δ 18O, MgCO 3 and Sr values. Na distinguishes between seawater and non-seawater influenced environments, but Fe, Mn and P are mainly controlled by non-carbonate materials. Comparison with published stable isotope and elemental data for Pleistocene limestones in the south Florida area suggests that only the facies diagnostic signatures of δ 13C and Mg will be resolvable once the muds have been stabilised to micrite. Alteration of the δ 18O and Sr values during stabilisation will probably be more severe, to the extent that original facies variations are destroyed.