In natural deltaic settings, mixed hydrodynamic forcings and sediment properties are known to influence the preserved delta deposits. One process that has not received much attention yet is syn-sedimentary compaction of clastic sediment on millennial-scale delta evolution. To study how compaction interacts with delta morphodynamics and preserved sediment, a modelling approach is proposed. A 1D grain-size dependent compaction model was implemented into Delft3D-FLOW, which provides an opportunity to understand the underexplored connection between grain sizes supplied to the deltas and sediment compaction. The compaction model allows deposited sediment to decrease in volume due to the accumulation of newly deposited sediments above or the elapsed time. Differences in morphological trends are presented for scenarios defined by the composition of sediment supply (mud rich and sand rich) and the maximum allowed compaction rate in the model (0–10 mm year−1). The resultant deposits are classified into sub-environments: delta top, delta front and pro delta. The delta top geometry (e.g. area increase, rugosity and aspect ratio), sediment distribution alongshore and across sub-environments, and delta top accommodation (e.g. volume reduction and average water depth) are compared. The modelling results show that compaction of the underlying delta front and pro delta deposits increases the average water depth at the delta top, driving morphological variability observed in the mud-rich and sand-rich deltas. The morphological changes are more prominent in the mud-rich deltas, which experience larger compaction-induced volume reduction for the same scenario. Moreover, higher compaction rates further increase the delta top accommodation, resulting in more deposition and evenly distributed sediment at the delta top. This leads to a less significant area increase and a wider delta top with a smoother coastline. The presented modelling results bridge the knowledge gap on the influence of syn-sedimentary compaction on long-term delta morphodynamics and preserved sediment. These findings can be applied to unravel the controlling processes in ancient delta deposits and predict the evolution of modern systems under changing climates.@en