Land reclamations influence the morphodynamic evolution of estuaries and tidal basins, because altered planform changes tidal dynamics and associated residual sediment transport. The morphodynamic response time to land reclamation is long, impacting the system for decades to centuries. Other human interventions (e.g., deepening of fairways or port construction) add a morphodynamic adaptation timescale to a system that may still adapt as the result of land reclamations. Our understanding of the cumulative effects of anthropogenic interference with estuaries is limited, because observations usually do not cover the complete morphological adaptation period. We aim to assess the impact of land reclamation works and other human interventions on an estuarine system by means of digital reconstructions of historical morphologies of the Ems Estuary over the past 500 years. Our analysis demonstrates that the intertidal-subtidal area ratio altered due to land reclamation works and that the ratio partly restored after land reclamation ended. The land reclamation works have led to the degeneration of an ebb- and flood channel system, transitioning the estuary from a multichannel to a single-channel system. We infer that the 20th-century intensification of channel dredging and re-alignment works accelerated rather than cause this development. The centennial-scale observations suggest that estuarine systems responding to land reclamations follow the evolutionary trajectory predicted by tidal asymmetry-based stability theory as they move towards a new equilibrium configuration with modified tidal flats and channels. Existing estuarine equilibrium theory, however, fails in linking multichannel stability to the loss of intertidal area, emphasizing the need for additional research.