Phytoplankton carbon-14 productivity at a depth of 50 percent of surface light and chlorophyll-a concentrations were measured every other month from November 1985 through September 1986 at 12 stations in the Charlotte Harbor estuarine system. Maximum productivity and chlorophyll-a concentrations occurred during summer or early autumn near the months of tidal rivers. Most of the variability in light-normalized productivity and chlorophyll-a could be attributed to two factors derived from Principal Component Analysis of ambient water-quality characteristics. One factor related to seasonal variability and the other to spatial variability. The seasonal factor incorporated the interaction of temperature and nutrients. The spatial factor incorporated the interaction of salinity, nutrients, and water color that resulted from the mixing of freshwater inflow and seawater. Although freshwater inflow increased the availability of nutrients in low salinity (less than 10 %) waters, the highly colored freshwater restricted light penetration and phytoplankton productivity. Maximum productivity and biomass occurred where color associated with the freshwater inflow had been diluted by seawater so that light and nutrients were both available. Concentrations of inorganic nitrogen were often at or below detection limit throughout most of the high salinity (greater than 20 %) waters of the estuary and was probably the most critical nutrient in limiting phytoplankton productivity.