Effective flood protection can be achieved only through the formulation of a trans-boundary cooperation strategy for flood risk management. The significance of the strategy will grow in future due to the emerging climate changes and their harmful consequences. The first step in flood-risk mitigation is the integration (trans-boundary, horizontal and vertical) of the efforts of all interested parties – stakeholders and local and regional authorities. This aim can be achieved only trough a trans-boundary, interdisciplinary and stakeholder-oriented approach. The project will gather together scientists, local and regional authorities, non-governmental organizations (NGOs) and stakeholders in the framework of the joint project in order to elaborate a common methodology and model for flood-risk assessment and mapping. This most cost-effective approach will result in concrete proposals for technical, economic and environmentally friendly flood-mitigation measures, a tool for planning and establishment of sustainable development in the catchments, raising awareness and interest among the societies for flood risk adaption.