To achieve water quality goals in a river basin, a water quality management model (WQMM) has been developed through the geographic information system (GIS) approach and a mathematical water quality model. The developed model has been applied to the Karun and Dez Rivers, where water quality has decreased due to heavy pollutant loads from Khuzestan province cities and surrounding areas. Pollution sources, land use, geographic features and measured water quality data of the river basin were incorporated into the Arc-View GIS database. With the database, the management model calculated management type and management cost for each management project in the river basin. Until now, river management policy for polluted rivers in Iran first penalizes pollution sources and then constructs treatment plants for the pollution sources whose wastewater is released untreated and for which the wastewater quality goal of the Iranian Department of Environment is not met. Different management projects with a time programme were proposed and they were compared with the results of the river quality without any management approach. It became clear that the results based on the management approach were much better than those for the unmanaged condition from the viewpoint of the achievement of water quality goals and cost optimization.