Peat growth is a frequent phenomenon in European river valleys. The presence of peat in the floodplain stratigraphy makes them hotspots of carbon storage. The long-term dynamics of alluvial peatlands are complex due to interactions between the peat and the local river network, and as a result, alluvial-peatland development in relation to both regional and local conditions is not well understood. In this study, a new modelling framework is presented to simulate long-term peatland development in river floodplains by coupling a river basin hydrology model (STREAM – Spatial Tools for River basins and Environment and Analysis of Management options) with a local peat growth model (modified version of DigiBog). The model is applied to two lowland rivers in northern Belgium, located in the European loess (Dijle (Dyle) River) and sand (Grote Nete River) belts. Parameter sensitivity analysis and scenario analysis are used to study the relative importance of internal processes and environmental conditions on peatland development. The simulation results demonstrate that the peat thickness is largely determined by the spacing and mobility of the local river channel(s) rather than by channel characteristics or peat properties. In contrast, changes in regional conditions such as climate and land cover across the upstream river basin have been shown to influence the river hydrograph but have a limited effect on peat growth. These results demonstrate that alluvial-peatland development is strongly determined by the geomorphic boundary conditions set by the river network and as such models must account for river channel dynamics to adequately simulate peatland development trajectories in valley environments.