Yes, there is a
shortage of water, that may be alleviated by new discoveries of underground aquifers. But there are always shortages. Scarcity is the essential problem of economics.
As the linked article notes, if the government in Khartoum tries to centralize control of the new water supplies (and as it doesn't note, if it continues to be an Arab nationalist government) further conflict is almost a given, no matter how much water was found.
Ethnic conflict occurs when the inevitable resource conflict cannot be solved by mutually agreeable means. The US has multiple ethnic groups, but as long as there is a political system, including a court system, acceptable to everyone, conflict won't spill over into the streets. That's one major reason why the Civil Rights Movement to integrate minorities into the system was so important.
As long as the government in Khartoum is Arab nationalist there will be a disaffected minority. But as a matter of fact, Arabs themselves are a minority in the Sudan, so there will be a disaffected majority. Until Khartoum accepts African nationalism, and realizes that Arabs are just another ethnic group, not THE acceptable, legitimate group, there will be ethnic conflict in the Sudan. That's one reason the ultimate responsibility for policing Darfur must become the primary responsibility of the AU.
Another reason is that any foreign peace-keeping mission is only temporary. You cannot expect a Kashmir or Cyprus style UN force to be there indefinitely without cease fire lines. This is more like Bosnia.
That means either an African Union force, or more realistically a federal force from some kind of a United States of Africa, has to stay there to police the area, because we know the Sudanese government is one sided in their approach. They have to be, as long as they are committed to Arab nationalism, which is ethnically specific in content from the beginning.