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This study presents a detailed reconstruction of the palaeogeography of the Rhine valley (western Netherlands) during the Holocene transgression with systems tracts placed in a precise sea-level context. This approach permits comparison of actual versus conceptual boundaries of the lowstand, transgressive and highstand systems tracts. The inland position of the highstand Rhine river mouth on a wide, low-gradient continental shelf meant that base-level changes were the dominant control on sedimentation for a relatively short period of the last glacial cycle. Systems in such inland positions predominantly record changes in the balance between river discharge and sediment load, and preserve excellent records of climatic changes or other catchment-induced forcing. It is shown here that the transgressive systems tract-part of the coastal prism formed in three stages: (i) the millennium before 8·45 ka bp, when the area was dominated by fluvial environments with extensive wetlands; (ii) the millennium after 8·45 ka, characterized by strong erosion, increasing tidal amplitudes and bay-head delta development; and (iii) the period between 7·5 and 6·3 ka bp when the Rhine avulsed multiple times and the maximum flooding surface formed. The diachroneity of the transgressive surface is strongly suppressed because of a pulse of accelerated sea-level rise at 8·45 ka bp. That event not only had a strong effect on preservation, but has circum-oceanic stratigraphical relevance as it divides the early and middle Holocene parts of coastal successions worldwide. The palaeogeographical reconstruction offers a unique full spatial–temporal view on the coastal and fluvial dynamics of a major river mouth under brief rapid forced transgression. This reconstruction is of relevance for Holocene and ancient transgressive systems worldwide, and for next-century natural coasts that are predicted to experience a 1 m sea-level rise.