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Training walls to improve navigability at river mouths alter natural sediment transport regimes, occasioning morphological changes in the nearby littoral zone. In addition, harbor channels and shorelines are susceptible to on-going changes in global circulation conditions and large-scale engineering interventions. Here we present a process-based modeling approach to determine the relationship between spatial patterns of erosion and deposition, seasonal river discharge, and the geometry of coastal defenses. The study uses the Magdalena River delta as an example, where the redistribution of freshwater and sediments after the construction of the "Tajamar" training wall heralded significant morphological changes in the area. The numerical experiments are used to describe how the erosion and deposition patterns within the estuary and delta of the Magdalena River are linked to the seasonal cycle of the Magdalena River and to the geometry of the hard structures. We demonstrate that the construction of the Tajamar and complementary hard structures would have decreased depositional fluxes in the littoral zone, leading to the observed shoreline retreat and disappearance of an extensive coastal lagoon system. It is shown that an aperture in the training walls may help restore the wetlands without compromising navigability. In addition, projected increases in mean sea level are shown to decrease velocities within the lower estuary, potentially causing increased sedimentation within the channel and more complex conditions for the management of safe navigation over the Magdalena River estuary. • Seawall construction on the Magdalena River, Colombia, resulted in the redistribution of freshwater and sediments. • Numerical experiments provide evidence that shoreline retreat was caused by the altered sedimentation regime. • A diversion system in the training walls may help restore sediment supply to the shorelines without risking navigability. • Sea level rise may increase rates of sedimentation within the estuary. [ABSTRACT FROM AUTHOR]