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Partial pressures of carbon dioxide (pCO2) were measured in river and coastal waters on two cruises in November 1999 and June 2000 on the Southwest Florida Shelf. Supersaturation with respect to the atmosphere was observed for most river and near-shore waters in November 1999. pCO2 ranged from 403 μatm in the Gulf of Mexico to 1280 μatm in the Shark River. The coastal waters of the Southwest Florida Shelf had unusually low salinities at this time due to high inputs of freshwater runoffs after Hurricane Irene. In general, pCO2 levels decreased with increasing salinity, but at different gradients for the different river systems. In June 2000, salinity gradients were considerably reduced during this drought year, with hypersalinity indicating reduced freshwater inputs. However, high pCO2 levels were still observed in and near the mouth of the Shark River (pCO2=383–1280 μatm). A positive correlation of pCO2 levels with colored dissolved organic matter (CDOM) and chlorophyll was observed in all systems examined. CO2 in natural waters may be produced from the photochemical degradation of CDOM, microbial respiration or via shifts in the carbonate equilibrium. Some evidence for a small contribution from photochemical production was observed in the Shark River mouth in a dry season diel study, but not in the wet season. Differences between the rivers are primarily attributed to the significantly higher total alkalinity and lower pH values in the Shark River, and associated higher pCO2 levels. In general, spatial variability in pCO2 is dominated by the chemical characteristics of the river inputs, with temporal variability modulated by changes in pH, photochemical production in low flow seasons and draw down by primary production. [Copyright &y& Elsevier]