Achieving sustainable management of water resources is a conscious social decision that provides long–term durability of a watershed regarding ecological and economical means. The limited capacity of the world’s water resources as an important natural capital (NC) cannot meet the growing demands of the socio-economic system (SES) without setting a strategy of sustainable management. One of the simplest solutions of the problem that is applied in many countries is water transfer from a rich water resource to another. Interbasin transfer of water can simply be described as the transfer of water artificially from one basin to another through a pipeline or a canal. Interbasin water transfers are a common component of many regional water systems. It has been in use for a long time all over the world. At present, a great number of various water transfer systems operate or are under construction for urban drinking water supply, irrigation, industry and environmental rehabilitation. Although it is clear enough that an underlying premise to this decision is the recognition of the interdependence between NC and SES that directly or indirectly influences the ecosystem, this important link is not taken into consideration in Turkey during decision making process with the goal of developing a long-term integrated plan for sustainable management of both watersheds. In this study, a reliable and simple decision support system was developed to help decision makers about interbasin water transfer. The first stage of the support system is the investigation of alternatives water resources. Reuse of urban waste water, desalination, rainwater harvesting and water demand management should be evaluated as a water resources and then transfer decision should be made. This subject is the main topic of water resources management that it was not evaluated within the context of this study. In the second stage the transfer decision is evaluated in details. After this stage it is possible to produce knowledge for decision makers about interbasin transfer is possible or not, and if it is, what would be the amount of water transferred, types of transfer (permanent transfer, contingent transfer). The decision support system was developed following three basic principles: First, the area of delivery must face a substantial deficit in meeting present or projected future water demands after consideration is given to alternative water supply sources and all reasonable measures for reducing water demand. Second, it will be provided that there will not be any substantially degradation of environmental quality in the donor basin. There will not be any destruction in habitat of living organisms that is under protected and economically valuable. Third, transfer will be possible, when the future development of the donor basin must not be substantially constrained by water scarcity. However consideration to transfer that constraints future development of donor basin may be appropriate if the receiving basin compensates the donor basin productivity losses. It is aimed that the support system should be appropriate to Turkey’s condition and must be reliable, simple and admitting of rapid assessment. Furthermore, the developed decision support system was implemented to Büyük Melen Water Transfer Project (Water transfer from Büyük Melen River to Istanbul) as an example. As a result of developed decision support system, to prevent degradation of ecosystem quality in the downstream of the diversion point of Büyük Melen River flow rate should be 18 m3/s at least. It is planned that the amount of the transferred water will be 8.50 m3/s at the first stage. For this reason the amount of transferred water must be 3.40 m3/s and 4.84 m3/s in July and October respectively, and this result indicates that water must not be transferred in August and September from the river. In the last stage of the projects the amount of transferred water should be as follows to prevent degradation of aquatic ecosystem: 34.74 m3/s in May, 13.40 m3/s in June, 3.40 m3/s in July, 4.84 m3/s in October transferred and no transfer in August and September. In this condition the average flow rate of transfer is 32 m3/s. It is planned that the amount of the transferred water will be 37.50 m3/s at the last stage. This planned flow rate is bigger than flow rate which is calculated with the developed support system. As a result Büyük Melen River ecosystem will be affected if the proposed action plan is not considered.