Three estuaries near Naples, Florida with variably modified watersheds have been investigated to understand die chemical consequences of altering drainage patterns. Blackwater River (near natural drainage, control site), Henderson Creek (moderately modified watershed), and Faka-Union Canal (severe channelization) were sampled for temperature, salinity, delta(18)O, delta(13)C of dissolved inorganic carbon (DIC), molality of CO2 (SigmaCO(2)), and Mg:Ca and Sr:Ca ratios between freshwater and marine water end members over a 17-mo period. Carbon isotope composition followed similar seasonal patterns as salinity. Freshwater and seawater end members are more negative than the global average, likely reflecting equilibration with local carbon sources derived from mangrove leaf litter and groundwater. delta(13)C responds to differences in primary productivity between estuaries. Henderson Creek has higher primary productivity than Blackwater River (probable due to higher sewage input and agricultural runoff) and has more positive delta(13)C and lower SigmaCO(2). delta(18)O is affected by seasonal input of freshwater from atmospheric precipitation, evaporation, and groundwater. Late summer and fall rains lower the delta(18)O of estuarine water, whereas evaporative conditions in the dry season elevate delta(18)O to values that can be more positive upstream than those from the Gulf of Mexico (estuarine inversion). Evaporation produces water in the Gulf of Mexico that is > 1parts per thousand more positive than the global sea surface average most of the year. The very negative delta(18)O values in Blackwater River and Henderson Creek likely reflect atmospheric and groundwater contribution. Mg:Ca and Sr:Ca ratios of Gulf water from all three estuaries are similar to global averages at low latitudes. Freshwater end members among estuaries are different in that Blackwater River has higher ratios, suggesting a groundwater contribution. Dolomitic rocks in the subsurface likely provide a source of Mg ions.