Field observations and culture experiments have been carried out during the rainy season (on the 6th, 8th and 27th July 2009) to examine changes in the primary productivity and associated plant pigments in the estuary of the Seom-jin River. Primary productivity was determined at four sampling stations along the salinity gradient. On 6th July (before heavy rain) primary productivity ranged from 689~1,169 mgC m-2 d-1. On the 8th, just after more than 216.5 mm of precipitation, euphotic layers at all stations were reduced to very shallow water because of the high concentration of suspended solids in the water. This resulted in dramatically decreased primary productivity down to as low as 12~32 mg C m-2 d-1. However, after the rain, primary productivity on the 27th ranged from 266~999 mgC m-2 d-1, demonstrating a fast recovery in the upper stream water to similar productivity levels to those before the rainy season. Concentration of fucoxanthin in the water was highest on the 6th July. Before the rain, concentration of the zeaxanthin, increased as the salinity decreased. Immediately after the heavy rain, the Chl b (Chlorophytes) concentration was higher at all sites than before the rainy season. The concentration of fucoxanthin decreased after the heavy rain. At the downstream site, peridinin (Dinoflagellates) were found. During the rainy season, the diatoms contributed to the primary productivity at all sites. However, after the rainy season, Chl b (Chlorophytes) and Peridinin (Dinoflagellates) increased, demonstrating the enhanced contribution of those species in addition to diatoms.