Abstract. Understanding the alterations in spatial–temporal water level dynamics caused by natural and anthropogenic changes is essential for water resources management in estuaries, as this can directly impact the estuarine morphology, sediment transport, salinity intrusion, navigation conditions, and other factors. Here, we propose a simple triple linear regression model linking the water level variation on a daily timescale to the hydrodynamics at both ends of an estuary. The model was applied to the upper Yangtze River estuary (YRE) to examine the influence of the world's largest dam, the Three Gorges Dam (TGD), on the spatial–temporal water level dynamics within the estuary. It is shown that the regression model can accurately reproduce the water level dynamics in the upper YRE, with a root mean squared error (RMSE) of 0.061–0.150 m seen at five gauging stations for both the pre- and post-TGD periods. This confirms the hypothesis that the response of water level dynamics to hydrodynamics at both ends is mostly linear in the upper YRE. The regression model calibrated during the pre-TGD period was used to reconstruct the water level dynamics that would have occurred in the absence of the TGD's freshwater regulation. Results show that the spatial–temporal alterations in water levels during the post-TGD period are mainly driven by the variation in freshwater discharge due to the regulation of the TGD, which results in increased discharge during the dry season (from December to March) and a dramatic reduction in discharge during the wet-to-dry transitional period. The presented method to quantify the separate contributions made by changes in boundary conditions and geometry to spatial–temporal water level dynamics is particularly useful for determining scientific strategies for sustainable water resources management in dam-controlled or climate-driven estuaries worldwide.