Integrated Basin Flow Management (IBFM) approach has been proposed by Mekong River Commission (MRC) to balance the economic and social developments, and maintenance of productive, healthy ecosystems in the Mekong Basin. The IBFM approach needs analytical tools to be used in solving real management problems. Mathematical models, in this case hydrological, hydrodynamic, and water quality models, are among those tools. While such models are useful in themselves, their full potential is only realised when linked with social, economic and policy issues. This paper focuses on the estimating impacts of the development scenarios on natural resources and on socio-economy with the help of mathematic modelling. The work presented here is part of the WUP-FIN project, complementary project for Water Utilization Programme under MRC. WUP-FIN focuses on developing and implementing hydrological, environmental and socio-economic modelling tools for the Lower Mekong Basin impact assessment. The Mekong River is one of the largest rivers in the world having a catchment size of 795,000 km(2) and average flow of 14,500 m(3)/s (Mekong River Commission, 2003). The river is shared by six countries (from upstream): China, Myanmar, Lao PDR, Thailand, Cambodia, and Vietnam. The four latter countries form the Mekong River Commission which, following the MRC 1995 agreement (Mekong River Commission, 1995), was established to agree an equitable and sustainable use of water resources in the lower Mekong Basin (LMB). The Lower Mekong Floodplains is very complex system of rivers, channels, dykes, embankments and large areas of floodplains. In order to be able to simulate this system comprehensively, including the different hydrodynamic conditions and water quality calculations into the same model, a hybrid 1/2/3 D model system is needed. Here 3D EIA Flow Model for floodplains (Koponen et al., 2004) is coupled with 1/2D channel model. The focus is in two target areas in the LMB floodplains: Tonle Sap Lake and floodplain (Cambodia) and Mekong Delta (Vietnam). The following development scenario indicators have been used in the project: Flood characteristics: duration, area, arrival time, depth Dissolved oxygen Total suspended solids and net sedimentation Dry season water quality One of the main aims of the modelling in the project is to assess the possible impacts of upstream developments, especially the hydropower dams and reservoirs, on lake's ecosystem. The main impacts of the development will most probably be the changes in hydrological regime reducing the water level during floods and reducing the area of the inundated habitats. The upstream reservoirs may trap significant part of the sediments as well. This may impact such ecosystem productivity among other impacts, as bank erosion etc. The approach for integration between socio-economy, ecology and hydrology can be carried out with two different methodologies that are based on data and modelling, and on experience and knowledge. The context of the integration consists of geographical area and of a specific analysis tool (GIS) coupled with the model results (Nikula, 2005). Ecology acts as a connecting factor between socio-economy and hydrology.