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This paper explores the evolving patterns of hydropolitical relations in the dynamic contexts of Yarmouk and Blue Nile Rivers in comparison. The analysis aims at shedding light over the complex implications that recent political and social changes have aroused for the water disputes between Jordan and Syria on the one hand, and Ethiopia and Egypt on the other. In both basins, cooperative efforts toward the integrated management of transboundary waters have been only partially effective and largely undermined by the perpetuation of unilateral actions by riparian states. In the case studies, the lack of a basin-wide vision over the control and use of shared waters has resulted in disputes among the basin states and ultimately in an unsustainable, unfair, and unwise utilization of the resources. This paper argues that a substantive and effective integration of national water policies is unlikely to occur, unless power asymmetries are properly addressed in order to overcome the likelihood of hegemonic regimes.