In the Nile River Basin, upstream runoff variability is an acute issue to downstream countries, since these countries are almost entirely dependent on Nile waters. Cooperative management of the Nile waters has become urgent, considering climate variations (Conway, 2005; Yates & Strzepek, 1998 a) and the necessity to use the water resource for irrigation and hydropower. The Grand Ethiopian Renaissance Dam is currently under construction in Ethiopia not far from the border with Sudan (The dam speech, 2011; Hassaballah et al., 2011). The water resource in the Blue Nile River Basin is under increasing pressure due to rapid population and economic growth, which is often aggravated by a lack of coordinated management and governance. Incomplete knowledge of water uses and needs is the main obstacle for proper management of the water resource in poorly studied river basins. Hydrodynamic models, supported by field measurements, are often the most appropriate tool to study the water distribution in river networks, under high and low flow conditions, taking into account water uses, presence of structures, like weir and dams, as well as physical features, like the complex river network geometry. The objective of this research is to study the water distribution along the entire Blue Nile River system to quantify the availability of the water resource at all flow conditions.