<p>Understanding the self-adaptive adjustment mechanisms underlying shifts in hydrodynamic regimes and their responses to human interventions is critical for effective estuarine management. However, the impacts of boundary changes, such as upstream and downstream dynamic boundaries, and morphological boundaries—on residual water levels remain insufficiently explored. In this study, we utilize the MIKE 21 hydrodynamic model in conjunction with an analytical model to quantify the spatiotemporal evolution of residual water levels in the Pearl River Estuary (PRE) under various boundary condition scenarios. By Chebyshev Polynomials, residual water levels are decomposed into three components: the riverine factor (<i>Z</i>_r), the tide-riverine factor (<i>Z</i>_tr), and the tidal factor (<i>Z</i>_t). The results reveal a notable decrease in the contribution of <i>Z</i>_tr from dry to flood seasons, with average differences of 22% and 16% along the West and North River channels, respectively, indicating pronounced tide-river dynamics. Numerical experiments simulating variations in river discharge, relative sea level, and bathymetry further demonstrate how boundary condition changes modulate residual water levels through adjustments in tide-river interactions. Additionally, the underlying mechanisms driving hydrodynamic regime adjustments are elucidated by analyzing the spatial shifts in the contributions of <i>Z</i>_r and <i>Z</i>_tr across different scenarios. The strong agreement between model outputs and observations underscores the utility of combining numerical and analytical approaches to disentangle riverine, tidal, and tide-river dynamics. These findings provide valuable insights into the impacts of human interventions on estuarine hydrodynamics and offer scientific guidelines for sustainable water resources management in the PRE and the broader Guangdong-Hong Kong-Macao Greater Bay Area.</p>