Situated in the Upper Nile region, the affected area is home to more than 150,000 refugees from Sudan, the UN High Commissioner for Refugees (UNHCR) said in a statement.
The UN agency said floodwaters have submerged major roads, making access to the refugee camps difficult and leading to closer of schools.
The floods have also impacted access to public services, including hospitals and damaged sanitation facilities, increasing health risks.
"We remain concerned that the flooding may increase the risks and spread of diseases. South Sudan was recently declared cholera free last year with the fears that the deadly disease could make a comeback," UNHCR said.
South Sudan's northeast region is prone to floods, but the latest devastation is caused by heavy rains after rivers flowing from highlands in neighboring Ethiopia burst their banks.
UNCHR said the affected population is in dire need of humanitarian assistance as people have fled their homes, carrying along their belongings, and are gathering together on little islands of dry ground.
UNHCR has pre-positioned emergency shelter kits and material assistance to help more than 5,000 affected families to rebuild and repair damaged shelter, but more support is needed, the refugee agency added.
According to UNHCR, the conflict-torn east African country which has been at war since 2013 currently hosts almost 300,000 refugees mainly from Sudan's Blue Nile and South Kordofan.
Some 1.5 million people are internally displaced inside the country.