The rapid increase in dam construction has resulted in a worldwide loss of natural river flows. Regulated dam discharge into estuaries can interrupt the spatiotemporal occurrence of brackish communities adapted to optimal salinity ranges, further threatening biodiversity and ecosystem function in the affected regions. We used annual survey records from the Nakdong River Estuary from 2009 to 2018 to identify the indirect effect of regulated dam discharge on plants and migratory waterfowl. Increased mean salinity during the spring season negatively influenced the area covered by plants and the number of days on which swans were present during winter. Moreover, the mean salinity during the early growing periods of plants providing food to waterfowl was regulated by the amount of freshwater discharge from the estuarine barrage rather than by the direct effect of precipitation. Conservation managers should consider the amount of dam discharge and the salinity conditions during spring to maintain sufficient food resources and supporting functions for migratory waterfowl in the estuary. Our study highlights the need for a comprehensive assessment of time‐lag effects to minimize the negative impacts resulting from regulated dam discharge.