With poor sanitation, there are fears of waterborne diseases breaking out.
The South Sudan government has declared a state of emergency in 27 flood-affected areas.
The presidency said that the state of emergency was to allow humanitarian organisations access people in the affected areas.
French medical charity Medecins Sans Frontieres (MSF) estimates about 900,000 people have been affected by the heavy rains across the country since July.
In Pibor, one of the worst affected areas in the eastern region, roads have been cut off and bridges swept away, rendering them inaccessible.
With poor sanitation, there are fears of cholera and other waterborne diseases breaking out.
“The space is increasingly congested, thick with mud, has no latrines and just one functioning borehole. Some people are left with no alternative but to drink from the same open and contaminated water sources as they are washing in,” MSF said in a statement on Thursday.
The charity group said its response to medical and humanitarian needs was hampered by lack of space for additional makeshift clinics.
“There’s also no space to store a large supply of medicines and no cold chain capacity.
Some seven million people are in need of humanitarian assistance in South Sudan, according to the UN.
The country plunged in to civil war in 2013 after President Salva Kiir accused Vice President Riek Machar of plotting a coup.
The warring parties have since signed numerous peace deals, the latest of which is hoped to culminate in an inclusive transitional government on November 12.