The sedimentology, mineralogy and pore fluid chemistry of seven cores from the Holocene sediments of Florida Bay were studied to determine the physical processes and diagenetic reactions affecting the sediments. The cores were taken in a transect from a shallow mudbank onto a small adjacent island, Jimmy Key. Steady state models of pore fluid chemistry are used to estimate the rates of various reactions.

In the mudbank sediments, little carbonate mineral diagenesis is taking place. No change in sediment mineralogy is detectable and pore water profiles of Ca2+, Mg2+ and Sr2+ show only minor variation. Chloride concentrations indicate substantial biological mixing of seawater from the bay into the sediments in one of the cores. Pore water analyses of sulphate and alkalinity show only a low degree of sulphate depletion and a decreasing extent of sulphate reduction downcore. Models of sulphate reduction in the mudbank show that there is substantial chemical exchange between the sediment pore fluids and water from the bay probably as a result of bio-irrigation. The sulphate and alkalinity data also suggest that the underlying Pleistocene rocks contain water of near normal seawater composition.

Stratigraphic analysis and δ13C analyses of the organic carbon in the sediments of the island cores show that the sediments were primarily deposited in a subtidal mudbank setting; only the upper 20–30 cm is supratidal in origin. Nevertheless, island formation had a significant effect on pore fluid chemistry and the types of diagenetic reactions throughout the sediment column. Chloride in the sediment pore fluids is more than twice the normal seawater concentrations over most of the depth of the cores. The constant, elevated chloride concentrations indicate that hypersaline fluids which formed in ponds on the island are advected downward through the sediments. Models of the chloride profiles yield an estimate of 2·5 cm yr−1 as a minimum advective velocity. Changes in pore water chemistry with depth are interpreted as indicating the following sequence of reactions: (1) minor high-Mg calcite dissolution and low-Mg calcite precipitation, from 0 to 35 cm; (2) Ca- or Mg-sulphate dissolution and low-Mg calcite precipitation, from 5 to 35 cm; (3) dolomite or magnesite precipitation together with sulphate reduction, from 35 to 55 cm; and (4) little reaction below 55 cm. In addition, one or more as yet unidentified reactions must be taking place from 5 to 55 cm depth as an imbalance in possible sources and sinks of alkalinity is observed. The imbalance could be explained if chloride is not completely conservative. Despite the pore fluid chemical evidence for diagenetic reactions involving carbonate minerals, no changes in sediment mineralogy were detected in X-ray diffraction analyses, probably because of the comparatively young age of the island.