"Vast areas of [South Sudan] along the River Nile are now under water" according to the UN's humanitarian coordinator for the country Alain Noudéhou.
The UN estimates that 600,000 people in the country have been forced to leave their homes.
Returning from a visit to some of the flooded areas, Mr Noudéhou said that the number of people needing help "will continue to grow in the coming weeks, and many women and children who had earlier been displaced by sub-national violence are now displaced again".
One of the worst hit areas is Jonglei state where the "situation is dire", Mutya Masku, from the International Organization for Migration said.
Aid agencies are appealing for more help in dealing with the situation.
Further upstream, in Sudan, flooding has has also affected hundreds of thousands of people.
Experts said the Nile had reached levels not seen for a century.