This paper presents a model of the complex Magdalena River system, as an important step towards knowledge-based river management and flood risk management in Colombia, with due attention for both human and ecosystem interests. Rio Magdalena is the largest river of Colombia. It drains a catchment of 257,000 square kilometers and is home to 38 million people. Anthropogenic use of the floodplain areas conflicts with the natural value of these areas. On the one hand there are the extended ecosystems with unique wildlife species