An 800-year-long environmental history of Biscayne Bay, Florida, is reconstructed from ostracod faunal and shell geochemical (oxygen, carbon isotopes, Mg/Ca ratios) studies of sediment cores from three mudbanks in the central and southern parts of the bay. Using calibrations derived from analyses of modern Biscayne and Florida Bay ostracods, palaeosalinity oscillations associated with changes in precipitation were identified. These oscillations reflect multidecadal- and centennial-scale climate variability associated with the Atlantic Multidecadal Oscillation during the late Medieval Climate Anomaly (MCA) and the Little Ice Age (LIA). Evidence suggests wetter regional climate during the MCA and drier conditions during the LIA. In addition, twentieth century anthropogenic modifications to Everglades hydrology influenced bay circulation and/or processes controlling carbon isotopic composition.