Abstract Carbonate sediment cores from nearshore shallow water environments in Bermuda were collected in June 1977 Pore waters were removed and processed in a nitrogen atmosphere at in situ temperatures to prevent any sample processing artifacts and Ca 2+ , Mg 2+ , pH, SO 4 2− , titration alkalinity, salinity, PO 4 3− , NH 4 + and F − were determined. Stoichiometric nutrient regeneration models suggest that observed PO concentrations are considerably lower than calculated values The ion activity product lAP of fluorapatite in the pore fluids is substantially greater than the K sp indicating a supersaturation with respect to the fluorapatite mineral phase Inorganic and organic phosphate analyses of the sediments show large concentrations of both with C/P ratios lower than the normally observed ones for biogenic calcium carbonate minerals. These data strongly suggest phosphate removal from the pore water during diagenetic transformation of the organic matter (i.e. during microbial metabolism) and incorporation in fluorapatite mineral phases associated with calcium carbonate in the sediments Such processes may be the most important factor in apatite formation in organic rich shallow water carbonate regimes