Many aquatic ecosystems suffer from anthropogenic disturbances, including the introduction of damaging levels of toxic substances. The effects of disturbances include complex relations with various components involved in the systems, and can include physical, chemical, and hydrological disruption depending of the contaminant. Decision Support Systems (DSSs) are developed to help decision makers to deal with complex management crises, through the systematic structuring and evaluation of decisions, and through providing easy-to-use and integrated tools for information elaboration and display. We reviewed various DSSs developed for toxic substances in aquatic ecosystems, and suggested a conceptual framework which is best suited to the management of such issues within Korea. It may assist stakeholders with their decision making process, and in the achievement of a consensus on water management solutions.