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Comparison of geo-referred bathymetric datasets from 2000 to 2017, at different timescales, allowed to analyze changes in the sedimentary balance and to determine patterns of morphological adjustment in the Magdalena River (South America). The Magdalena River has one of the highest sediment yields among the major rivers of the world. In addition, it is a laterally constrained river mouth due to a series of man-made structures inhibiting its morphological response. Thus, it provides an illustrative example to study siltation processes in a river mouth system where a low capacity of morphological response interacts with a high-magnitude sediment transport regime. The river mouth exhibited an overall slow-pace deepening trend between 2000 and 2017. However, it experienced cyclic shifts between erosive and siltation states, both at interannual and intra-annual scales. The rates of erosion were 310 mm yr−1 on average during the erosional stages. Whereas sedimentation rates were 293 mm yr−1 on average during the sedimentation stages. Maximum rates of erosion and sedimentation were 1450 mm yr−1 and 2625 mm yr−1, respectively. However, intra-annual rates of sedimentation/erosion were of the same magnitude or larger compared with the interannual rates. Such high rates and the rapid changes in the sedimentary balance is the result of the cumulative effect of its limited morphological response capacity and its large suspended sediment load. These rapid processes generate constraints and threats to navigation. Particularly, at intra-annual scales. Consequently, innovative intervention proposals, recognizing the rapid transitions and geomorphological adaptations, are required for managing this type of river mouths. Image 1 • Comparison of geo-referred bathymetric datasets (2000–2017) at the Magdalena River (South America). • Magdalena river has a laterally constrained river mouth due to a series of man-made structures. • The river mouth exhibited an overall slow-pace deepening trend between 2000 and 2017. • River mouth experienced cyclic shifts between erosive and siltation states, at interannual and intra-annual scales. • Intra-annual rates of sedimentation/erosion were of the same magnitude or larger compared with the interannual rates. [ABSTRACT FROM AUTHOR]