Nice recap of the issues at hand.
The Khartoum declaration, which was signed by the heads of state of the three countries—Abdel Fattah al-Sisi (Egypt), Omar al-Bashir (Sudan), and Halemariam Desalegn (Ethiopia), has been referred to as a “Nile Agreement,” and one that helps resolve conflicts over the sharing of the waters of the Nile River. However, this view is misleading because the agreement, as far we know, only deals with the Blue Nile’s Grand Ethiopian Renaissance Dam project (GERDP) and does not tackle the broader, still contentious issues of sharing of the Nile River waters among all riparian states. Thus, the new agreement does leave the conflict over the equitable, fair, and reasonable allocation and utilization of the waters of the Nile River unresolved.
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Over the years, especially as the populations of the other countries of the Nile River Basin have increased, and these countries have developed the capacity to more effectively harvest the waters of the Nile River for national development, disagreements have arisen over the fact that Egypt has insisted that the water rights it acquired through the 1929 and 1959 agreements (collectively referred to as the Nile Waters Agreements) be honored and that no construction project be undertaken on the Nile River or any of its tributaries without prior approval from Cairo. In fact, various Egyptian leaders have threatened to go to war to protect these so-called “acquired rights.” Upstream riparian states such as Kenya, Tanzania, Uganda, and Ethiopia, have argued that they are not bound by these agreements because they were never parties to them.
The spectre of a "water war" is regularly bandied around the international media, but the possibility of it happening are actually really slim, both for military and political reasons. That is not to say that the issue of the Nile is not taken dead seriously by countries like Egypt, Sudan and Ethiopia. With all of the riparian states still in their economic infancy, this will remain a hot button issue for some time to come.
Source: The limits of the new “Nile Agreement” | Brookings Institution