The impact of physical habitat change on the river ecology has increasingly caused concerns in both academic and engineering communities. The hydro-morphological integrity is considered as a key issue because it affects both the ecological structures and functions. Due to its complexity, the relationship between the morphological and ecological processes is not fully understood, although many efforts have been made by researchers in related disciplines, including geologists, geo-morphologists, sedimentologists, hydraulic engineers etc. In this study a physics-based mathematical model has been developed to simulate the fluvial morphological processes. In this model, two dimensional shallow water equations are solved using a TVD scheme, which is suitable for a wide range of flow conditions. A non-uniform sediment transport model is applied to simulate the evolution processes of an alluvial river, in which the sediment sorting process can be predicted. The colonization of vegetation can change the bank and bar stability, which plays an important role in the evolution of river planform, including bars, sub-channels, confluences, bifurcations and even complex river networks. These morphological processes, in return, affect the spatial and temporal distributions of vegetation growth and decay. In addition, the effects of hydrographs and sediment sorting have been investigated in these inter-relationships. As the substrate and habitat to the aquatic ecology system, eco-environmental factors along morphological units have been investigated using the present model, including the sediment properties on pools and bars, the velocity distributions, the changes in riffles and bends and the vegetation encroachment on banks and bars.