The morphodynamic system in alluvial, coastal plain estuaries is complex and characterized by various timescales and spatial scales. The current research aims to investigate the interaction between these different scales as well as the estuarine morphodynamic evolution. Use is made of a process-based, numerical model describing 2-D shallow water equations and a straightforward formulation of the sediment transport and the bed level update. This was done for an embayment with a length of 80 km on a timescale of 3200 years, with and without bank erosion effects. Special emphasis is put on analyzing the results in terms of energy dissipation. Model results show that the basins under consideration evolve toward a state of less morphodynamic activity, which is reflected by (among others) relatively stable morphologic patterns and decreasing deepening and widening of the basins. Closer analysis of the tidal wave shows standing wave behavior with resonant characteristics. Under these conditions, results suggest that the basins aim for a balance between the effect of storage and the effect of fluctuating water level on wave celerity with a negligible effect of friction. Evaluating the model results in terms of energy dissipation reflects the major processes and their timescales (pattern formation, widening, and deepening). On the longer term the basin-wide energy dissipation decreases at a decreasingly lower rate and becomes more uniformly distributed along the basin. Analysis by an entropy-based approach suggests that the forced geometry of the configurations prevents the basins from evolving toward a most probable state.