Analyses of 203 samples of benthic foraminifera in six cores from four sites in Florida Bay indicate habitat change over the last ~4000 years. Sample ages were determined for the last ~120 years with 210Pb, and for up to ~4000 years at two sites with 14C. The largest habitat changes upcore were identified with stratigraphically constrained cluster analysis (CONISS), which evaluates the similarity of vertically adjacent samples. Paleoenvironmental interpretations of habitat changes were mostly based on varying proportions of two defined associations of environmental indicator taxa and changes in diversity. The timing of the interpreted environmental changes was compared to known natural and anthropogenic events to examine their correspondence and possible relationship.

The bay’s initial flooding ~4000 YBP was indicated at the offshore Ninemile Bank by a very high proportion of an Ammonia association and very low proportion of a Quinqueloculina association, similar to modern nearshore assemblages in Trout Cove, the core site closest to the mainland. Construction of the Florida Keys railroad in 1907–1910 led to restricted exchange with the open ocean; foraminifera indicate a salinity decrease at that time, probably from the increased influence of runoff. Faunal changes since the 1920s in central Florida Bay signify increasingly saline (>32 psu) waters. Between 1928–1938, concurrent peaks in the Ammonia association at all sites suggest widespread freshening of the bay, which corresponds to an unusual succession of three powerful, wet hurricanes between 1926–1938. After flushing of the bay by hurricanes, a long-term result of decreased circulation caused by railroad construction was the increased retention of organic materials in the bay; more organic-rich conditions after 1932 are indicated at Ninemile Bank by a shift in infaunal Bolivina species to their highest abundance. In the central bay after 1962, the amplitude of changes in the Ammonia association and diversity was greater, probably related to larger salinity shifts caused by increases in water management in addition to natural events such as droughts. In the central bay in 1987, decreases in diversity, increases in infaunal taxa and decreases in epiphytic species clearly reflect a severe, bay-wide seagrass die-off and drought. Thus, changes in Florida Bay habitats can be related to both anthropogenic and natural causes. Despite any degradation of water quality in the past 50 years, foraminiferal diversity has increased at most sites.

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