<p>Estuarine ecosystems are highly dynamic environments that provide critical ecological functions but remain vulnerable to anthropogenic pressures. In this study, we investigated long-term sedimentary processes and their geomorphological consequences on habitat dynamics of the sedge <i>Bolboschoenus planiculmis</i> (<i>Scirpus planiculmis</i>) in the Nakdong River estuary, South Korea. By integrating high-resolution habitat distribution mapping, surface sediment analyses, and lithostratigraphic reconstructions from two estuarine sediment cores, we reconstructed environmental changes in the estuary during recent decades. The results showed that major anthropogenic interventions, including the construction of estuary dams and the Four Major Rivers Project, significantly altered river discharge regimes, accelerated sedimentation rates, and triggered changes in sediment texture. These processes caused elevation increase in the intertidal zone and a gradual shift toward supratidal conditions, thereby reducing the extent of sedge habitat. Moreover, core-based stratigraphy revealed event-scale sedimentary pulses and hydroclimatic signals coinciding with periods of reduced discharge and increased marine influence. These findings indicate that human-induced geomorphological transformations, interacting with changing hydrodynamic regimes, reshaped this coastal wetland habitat. The sedimentological imprint of these changes underscores the value of geological archives for assessing ecological vulnerability and provides a basis for habitat restoration and estuarine management under future anthropogenic and climatic stressors.</p>