A number of wetland ecosystem-services valuation studies around the world have been carried out, however, most of these studies have focused on wetlands in developed countries and few have been conducted in Africa, particularly in South Sudan. Thus, this study is conducted to value ecosystem services and identify the role and interests of stakeholders of the Machar Marshes and the Sudd wetlands for sustainable wetland management in the Nile basin. Market price and benefit transfer approaches have been applied to value the wetlands biodiversity and ecosystem services, by adjusting for income and price differences. In addition to environmental valuation methods, we conducted stakeholder analysis. Accordingly, Machar Marshes wetland provides an estimated per annum economic value of $200 million, of which the provisioning services contributed about $61 million, regulating services $132 million, and biodiversity services $7.35 million considering the 2015 price as a base year. Similarly, the Sudd wetland provides an estimated per annum economic value of 2.3 billion, of which regulating is about $1.2 billion, biodiversity $857 million, provisioning $209 million, and transportation service $293,400. The findings show that the ecosystem services from the wetlands have benefits beyond the local communities. Thus, to maintain and ensure sustainable wetlands ecosystem services, stakeholders should play a significant role to implement alternative wetland development options through managing the existing institutional challenges. Ecosystem-services assessment and wetland development options suffer from weak institutional capacity due to prolonged conflicts and instability and physical inaccessibility to critical natural resources in the wetlands.