This work develops a two-dimensional hydro-morphological model which can be used to simulate river hydraulics and morphology with various vegetation covers. The model system consists of five modules, including a hydrodynamic model, a sediment transport model, a vegetation model, a bank failure model and a bed deformation model. The secondary flow effects are incorporated through additional dispersion terms. The core components of the model system solve the full shallow water equations; this is coupled with a non-equilibrium sediment transport model. The new integrated model system is validated against a number of laboratory-scale test cases and then applied to a natural river. The satisfactory simulation results confirm the model's capability in reproducing both stream hydraulics and channel morphological changes with vegetation. Several hypothetical simulations indicate that the model can be used not only to predict flooding and morphological evolution with vegetation, but also to assess river restoration involving vegetation. (C) 2016 Elsevier Ltd. All rights reserved.