Mixed bedrock-alluvial rivers can exhibit partial alluvial cover, which may play an important role in controlling bedrock erosion rates and landscape evolution. However, numerical morphodynamic models generally are unable to predict the pattern of alluviation in these channels. Hence we present a new two-dimensional depth-averaged morphodynamic model that can be applied to both fully alluvial and mixed bedrock-alluvial channels, and we use the model to gain insight into the mechanisms responsible for the development of sediment patches and patterns of bedrock alluviation. The model computes hydrodynamics, sediment transport, and bed evolution, using a roughness partitioning that accounts for differential roughness of sediment and bedrock, roughness due to sediment transport, and form drag. The model successfully replicates observations of bar development and migration from a fully alluvial flume experiment, and it models persistent sediment patches observed in a mixed bedrock-alluvial flume experiment. Numerical experiments in which the form drag, sediment transport roughness, and ripple factor correction were neglected did not successfully reproduce the observed persistent sediment cover in the mixed bedrock-alluvial case, suggesting that accounting for these different roughness components is critical to successfully model sediment dynamics in bedrock channels.