The aim of this paper is to reconstruct the evolution of the early to middle Holocene Rhine-Meuse river mouths in the western Netherlands and to understand the observed spatial and temporal changes in facies. This is achieved by constructing three delta wide cross-sections using a newly accumulated database with thousands of core descriptions and cone penetration test results, together with a large set of pollen/diatom analyses and OSL/ 14 C-dates. Most of the studied deposits accumulated in the fluvial-to-marine transition zone, a highly complex area due to the interaction of terrestrial and marine processes. Understanding how the facies change within this zone, is necessary to make correct palaeogeographic interpretations.We find a well preserved early to middle Holocene coastal prism resting on lowstand valley floors. Aggradation started after 9 ka cal BP as a result of rapid sea-level rise. Around 8 ka most parts of the study area were permanently flooded and under tidal influence. After 8 ka a bay-head delta was formed near Delft, meaning that little sand could reach the North Sea. Several subsequent avulsions resulted in a shift from the constantly retreating Rhine river mouth to the north. When after 6.5 ka the most northerly river course was formed (Oude Rijn), the central part of the palaeovalley was quickly transgressed and transformed into a large tidal basin. Shortly before 6 ka retrogradation of the coastline halted and tidal inlets began to close, marking the end of the early-middle Holocene transgression. This paper describes the transition from a fluvial valley to an estuary in unprecedented detail and enables more precise palaeo-reconstructions, evaluation of relative importance of fluvial and coastal processes in rapid transgressed river mouths, and more accurate sediment-budget calculations. The described and well illustrated (changes in) facies are coupled to lithogenetic units. This will aid detailed palaeogeographic interpretations from sedimentary successions, not only in the Netherlands, but also in other estuarine and deltaic regions.