Recently climate change causes greater disaster than before, and the conventional measures especially against flood disaster are not enough at present. Integrated measures of facilities and Information systems are reinforced to cope with these situations. This study describes a solution to the issues. Flood disaster mitigation system is designed and developed to mitigate the damages caused by flood disaster adopting meteorological data and geographic information systems (GIS). In the phase of requirements analysis, system dynamics (SD) techniques, such as Iceberg Model and causal loop diagram (CLD), were applied to clarify three leverage points (precipitation data observation, river level forecast, and evacuation/alarming issuing). Precipitation information was derived from MesoScale Model (MSM) data provided by the Japan Meteorological Agency, and river level forecast was conducted based on Urban Tank Model. Swiss Cheese Model, basin hydraulic control, necessity of information (software) and facilities (hardware) were adopted into the structure of the Iceberg Model. The test site of the system is planned in the basins of the Nogawa and Tama Rivers in Tama Area, Tokyo, Japan. This study relates to the 9th “Industry, Innovation and Infrastructure” and the 13th “Climate Action” of the sustainable development goals (SDGs) proposed by the United Nation (UN).