The White Nile burst its banks in the Sudanese capital of Khartoum on Monday, flooding homes and businesses in at least one district.
The streets of Kalakla in the south of the city were flooded.
There were no immediate reports of casualties, but the government urged residents to take precautions against potential flooding from the Blue Nile, which also flows past the city.
Days of heavy rainfall in the Ethiopian Highlands, the source of the river, and parts of Sudan caused both the White Nile and the Blue Nile to swell.
While Khartoum residents living close to the Blue Nile shored up their defences, it was the White Nile that flooded the city, largely because of its relatively weak embankments.
About 100 people died last year in flooding that destroyed thousands of homes across Sudan.
Last week, at least four people south and west of Khartoum died in accidents related to flooding and heavy rainfall.
The Blue Nile typically swells in July and August every year as a result of the rainfall on the Ethiopian Highlands.
Ethiopia is building a massive hydroelectric dam on the Nile about 20 kilometres from the border with Sudan.
Addis Ababa believes the Grand Ethiopian Renaissance Dam will help lift tens of millions out of poverty.
But Egypt and Sudan have been putting pressure on Ethiopia to enter a legally binding agreement on the filling and operation of the dam to minimise its effect on their share of the Nile, and protect against flooding.
Ethiopia says guidelines should suffice.
A decade of negotiations over the dam has not yet yielded a deal, with the latest round of talks breaking down in April. It has not yet been announced when the discussions will resume.