This paper proposes an operational flowchart for integrated water management in accordance with the EU Water Framework Directive (WFD), based on identified necessary components for efficiency, participation and legitimacy in environmental management decisions. The flowchart identifies general methodologies for answering these main questions and integrates thereby different types of water and environmental management tasks, including: 1)development of water management plans and action programs, as required by the WFD; 2)environmental evaluation of permit applications for various development projects; 3)remediation decisions for contaminated land. For these tasks, the flowchart clarifies the same main questions that need to be answered, and the methodology to answer them by quantitative scientific analysis and negotiated agreements among stakeholders. The proposed flowchart also provides a general methodology for operational coordination and systematisation of scientific information and quantification needs and tools in sustainable integrated water management.