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Apalachicola Bay is a shallow estuarine system enclosed by a chain of barrier islands on the west Florida shelf. It is important both ecologically and economically due to the high biological productivity in the bay. The bay is subject to fluctuations in salinity, temperature, and dissolved oxygen. Salinity fluctuations are beneficial to many organisms in the bay. Measurements in and around the bay are analyzed to give a general description of how the bay's hydrographic properties vary in space and time. A salinity model using conservation of mass and salt is constructed in order to describe how the bay's salinity changes due to various forcing mechanisms. The main factors affecting salinity in Apalachicola Bay are freshwater inflow from Apalachicola River, winds in the direction of the major axis of the bay, and to a lesser extent, tides. When smoothed with a ten day filter, the salt model results over the three year study period agree with observations in each side of the bay at a correlation between 0.8 and 0.9. Variations in the concentration of dissolved oxygen with time are also analyzed, and the processes driving these are wind speed, temperature, biological activity, and advection. During one period when tides affect the concentration of dissolved oxygen, a regressive model based on tidal velocity and light measured near the bottom agree with observation at a correlation of > 0.8.