The Soil and Water Assessment Tool, known as the SWAT model, is a GIS-based basin-scale model for simulating hydrological and water quality processes. It is a pseudo-physically based model that is capable of predicting long-term effects of land management. The model was applied to simulate rainfall-runoff process, streamflow pattern, soil erosion and sediment transport in the Lower Mekong River Basin. This paper reports the major findings of analysing the flow and sediment transport at major locations along the Mekong River and discusses the results from the first-cut preliminary analysis. In addition, the paper briefly describes the hydrology of the Mekong Basin in connection with the human impact on the basin's health and provides a critical review on the role of integrative models for the implementation of the IWRM concept.