A 160 year record of skeletal δ¹³C and δ¹⁸O was examined in a specimen of the coral Solenastrea bournonigrowing in Florida Bay. Variations in the δ¹⁸O of the skeleton can be correlated to changes in salinity while changes in the δ¹³C reflect cycling of organic material within the Bay. Based on the correlation between salinity and skeletal δ¹⁸O, we have concluded that there has been no long term increase in salinity in this area of Florida Bay over the past 160 years. Using salinity correlations between the various basins obtained from instrumental data, we have been able to extend our interpretations to other parts of Florida Bay reaching similar conclusions. In contrast to current ideas which have focused on changes in Florida Bay water quality over the past 20-yr history of the Bay as causative in its decline, we have determined that changes in water quality in this basin were already set in motion between 1905 and 1912 by the construction of the Florida East Coast Railway from Miami to Key West. The construction of the railway resulted in the restriction of the exchange of water between the Florida reef tract and the Gulf of Mexico causing Florida Bay to become more eutrophic. Evidence of this process is observed in the sudden shift to relatively lower δ¹³C values coincident with railway construction. Natural events also appear to have influenced the water in the Bay. Between 1912 and 1948 frequent hurricanes had the effect of increasing exchange of water between the Bay and reef tract and removing large quantities of organic rich sediments. However, since 1948 the number of hurricanes affecting the area has decreased and the products of the oxidation of organic material have been increasingly retained within the basin promoting the initiation of eutrophic conditions.