Abstract. Alluvial river estuaries consist largely of sand but are typically flanked by mudflats and salt marshes. The analogy with meandering rivers that are kept narrower than braided rivers by cohesive floodplain formation raises the question of how large-scale estuarine morphology and the late Holocene development of estuaries are affected by cohesive sediment. In this study we combine sand and mud transport processes and study their interaction effects on morphologically modelled estuaries on centennial to millennial timescales. The numerical modelling package Delft3D was applied in 2-DH starting from an idealised convergent estuary. The mixed sediment was modelled with an active layer and storage module with fluxes predicted by the Partheniades–Krone relations for mud and Engelund–Hansen for sand. The model was subjected to a range of idealised boundary conditions of tidal range, river discharge, waves and mud input. The model results show that mud is predominantly stored in mudflats on the side of the estuary. Marine mud supply only influences the mouth of the estuary, whereas fluvial mud is distributed along the whole estuary. Coastal waves stir up mud and remove the tendency to form muddy coastlines and the formation of mudflats in the downstream part of the estuary. Widening continues in estuaries with only sand, while mud supply leads to a narrower constant width and reduced channel and bar dynamics. This self-confinement eventually leads to a dynamic equilibrium in which lateral channel migration and mudflat expansion are balanced on average. However, for higher mud concentrations, higher discharge and low tidal amplitude, the estuary narrows and fills to become a tidal delta.