Spatial and temporal variations in physical and geochemical properties were measured in Blackwater River, a subtropical estuary, in southwest Florida, USA. The survey was conducted at different tidal stages (high tide, low tide and rising tide) during the dry season (Feb. 2001), the onset of the wet season (July 2001), and the dry down as water levels dropped (Nov. 2001). Temperature, pH, salinity, alkalinity, dissolved inorganic carbon (DIC), and d¹³C varied spatially across the estuary. However, there were no significant differences in the spatial relationships of measured parameters for different tidal stages during each sampling event. Seasonal measurements showed significant down river shifts in all the parameters measured due to seasonal watershed influx of freshwater from inland. The results of this study showed distinct regions in the estuary from the geochemistry. The headwaters region was dominated by seasonal fresh to saline water, the middle reaches was a mixing zone between inland and seawater and the lower estuary was characterized by seawater mixing. We were able to model freshwater-seawater mixing in the estuary using salinity and carbon during the onset of the wet season and the dry down period. This type of mixing model was inadequate in the dry season, however, due to the absence of a freshwater end member. We conclude from this study that watershed response to seasonal freshwater input was more important than tidal mixing in controlling the physical and chemical properties of the Blackwater River estuary.