The Youngsan River estuary was physically changed by the construction of a sea embankment at near the mouth of estuary. Weirs were also constructed recently in the freshwater zone and it was reported that algal blooms occur more frequently. The freshwater introduced into saltwater zone from sluice gates of the embankment affects water quality but it has not been addressed that how the freshwater inputs influence the health of marine ecosystem. In this study, we used the data of water properties and phytoplankton communities collected at three stations for 4 days including before the freshwater discharge, during the discharge and after 1 and 2 days of discharge events. WQI (water quality index), TRIX (trophic status index) and P-IBI (phytoplankton index of biotic integrity) were used to evaluate the ecosystem health and long-term data were also utilized to determine the criteria for P-IBI. The results showed that grades of the ecosystem health assessed by the indices were low at the station near the gates and increased as downstream. However, the temporal pattern of grades was different depending on methods. Grades of WQI and TRIX decreased during the discharge and restored after the discharge whereas the grades of P-IBI decreased slightly even after the discharge. This suggests that P-IBI is more applicable to estuarine systems where experience extreme change of water properties than WQI and TRIX since P-IBI includes phytoplankton that can respond quickly to the change.