Seasonal variations of various physicochemical components (temperature, salinity, pH, DO, COD, DOC, nutrients-silicate, DIN, DIP) and potential limiting factor for phytoplankton primary production were studied in the surface water of semi-enclosed Masan Bay. Seasonal variations of nutrient concentrations, with lower values in summer and winter, and higher in fall, are probably controlled by freshwater loadings to the bay, benthic flux and magnitude of occurrence of phytoplankton communities. Their spatial distributional patterns are primarily dependent on physical mixing process between freshwater and coastal seawater, which result in a decreasing spatial gradient from inner to outer part of the bay. In the fall season of strong wave action, the major part of nutrient inputs (silicate, ammonium, dissolved inorganic phosphorus) comes from regeneration (benthic flux) at sediment-water interface. During the summer period, high Si:DIN and Si:DIP and low DIN:DIP relative to Redfield ratios suggest a N- and secondarily P-deficiency. During other seasons, however, silicate is the potential limiting factor for primary production, although the Si-deficiency is less pronounced in the outer region of the bay. Indeed, phytoplankton communities in Masan Bay are largely affected by the seasonal variability of limiting nutrients. On the other hand, the severe depletion of DIN (relatively higher silicate level) during summer with high freshwater discharge probably can be explained by N-uptake of temporary nanoflagellate blooms, which responds rapidly to pulsed nutrient loading events. In Masan Bay, this rapid nutrient consumption is considerably important as it can modify the phytoplankton community structures.