Analysis of river tides in the YRE reveals strong river-tide interactions and non-linear modulation of tides by river discharge. River discharge alters tidal asymmetries and resultant tidal residual sediment transport. Analysis of morphodynamic modeling results exposes significant mechanisms inducing tidal residual sediment transport and controlling long-term morphodynamic development. Morphodynamic equilibria in 1D and 2D simulations can be defined by vanishing gradients of tidal residual sediment transports and meeting empirical morphodynamic relationships. This research indicates the value of numerical modeling in examining long-term morphodynamic development in millennia time scale. Understanding of the controls on morphodynamic behavior in estuaries under river and tidal forcing is to the benefit of managing estuaries’ functions in a long-term point of view.