Statistical comparison of modern molluscan fauna to down-core molluscan assemblages in four cores elucidates changes in the Florida Bay ecosystem during the past 100 to 200 years. Fluctuations within molluscan faunal dominance and diversity patterns suggest a response to changing environmental conditions. Faunal dominance patterns indicate an increase in salinity in the northern transitional zone, and possibly the eastern portion of Florida Bay. Distinctive faunal shifts recorded at Russell Bank occur approximately between 1913 and 1933 and at Bob Allen mudbank between approximately 1900 and 1910. The period from approximately 1930 to 1980 within these cores shows rapid and dramatic fluctuations in species dominance and faunal richness. Beginning around 1980, the mussel Brachidontes exustus, which can tolerate diminished water quality and a wide range of salinities, increases in percent abundance in the upper portion of all four cores and becomes the dominant species at Russell Bank and Bob Allen Mudbank.

While these fluctuations within assemblages are distinctive, they are not so profound that they represent a major shift in estuarine zonations within northern, eastern, and central Florida Bay during the past 100 to 200 years. The majority of the molluscan fauna that are present at the core sites today are generally present throughout the period of deposition. Fluctuations in the molluscan faunal record down-core primarily express changes in dominance and diversity within assemblages and do not reflect substantial changes in overall assemblages. It is these fluctuations in dominance and the appearance or disappearance of critical indicator species that are indicative of salinity changes.

Understanding the dynamics of an ecosystem and the natural range of variation in the system over an extended period of time is a critical component of effective restoration. Analysis of the modern environment provides a means to interpret biological data preserved in cores, and to determine the physical and chemical variations in the environment indicated by the biota. Knowledge of the past provides the best insight to predicting the impact of future change on the environment.