Persistent conflict and flooding sustain a risk of Famine (IPC Phase 5) in Upper Nile

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Acute food insecurity and malnutrition levels are deepening at the peak of the lean season in September, driven by the severe impacts of persistent conflict, expanding flood extent, economic deterioration, and a high returnee and refugee burden on household access to local food sources and life-saving humanitarian food assistance. Parts of Upper Nile and northern Jonglei states – particularly Nasir, Ulang, Panyikang, Longochuk, Fangak, and Canal/Pigi counties – remain of highest concern, with widespread Emergency (IPC Phase 4) outcomes and pockets of households in Catastrophe (IPC Phase 5) expected through the end of the projection period in January based on the significant reductions in harvest prospects due to conflict and weather shocks. There is a credible risk of Famine (IPC Phase 5) in these areas, given the sustained threat that a convergence of conflict, insecurity, and flood waters could further isolate populations from accessing food sources and worsen the prevalence of waterborne diseases such as cholera.
In additional areas where the impact of conflict and/or flooding has undermined local production and access to other local food sources, including parts of Upper Nile, Jonglei, Unity, Greater Pibor Administrative Area, Warrap, and Greater Equatoria, Emergency (IPC Phase 4) and Catastrophe (IPC Phase 5) outcomes are expected to persist through January. Outbreaks of diseases such as cholera are expected to remain a serious risk amid minimal basic health, water, and hygiene services, which is likely to sustain high levels of acute malnutrition through the projection period. In less conflict- and flood-affected areas in South Sudan, food security is expected to improve slightly amid the seasonal increase in the availability of the harvest and other food sources (livestock products, fish, wild foods) through January.
Clashes continued in late August through mid-September between South Sudan People’s Defense Force (SSPDF) and allied opposition forces in parts of Canal/Pigi and Ayod (Jonglei) and Nasir, Ulang, Panyikang, Baliet, and Longochuk (Upper Nile). Ground offensives and aerial bombardments are displacing populations, disrupting livelihood activities, and interfering with the delivery of assistance. Meanwhile, in the border area between Pibor and Eastern Equatoria’s Kapoeta North county, the raiding of over 80 herds of cattle in early September illustrates the persistent threat of violent retaliatory cattle raiding in this region. In other counties of Greater Equatoria, persistent violence in parts of Yei and Morobo (Central Equatoria), as well as clashes between SSPDF and Sudan People’s Liberation Army (SPLA-IO) in Tambura (Western Equatoria), are disrupting livelihood activities and trade flows. Finally, in Warrap State, FEWS NET observed during a September rapid field assessment that over 20,000 people remain internally displaced with limited access to food in Tonj East and Tonj North counties despite the return of relative calm in August and September. The displacement occurred as a result of months of escalating retaliatory intercommunal conflict and violent cattle raids since late 2024 that peaked in May and continued sporadically into August.
Recent heavy rains, above-average lake water levels upstream in Uganda, and swiftly rising Nile River water levels have led to a significant expansion of inundated areas, nearly doubling between early August and early September. By September 11, over 311,000 people in 13 counties across four states had been affected by floods, with Jonglei and Unity states accounting for over 87 percent of those affected. The floods have destroyed homes, displaced households, submerged crops, and disrupted access to basic health and nutrition services. In Fangak, the collapse of a dyke on August 30 led to severe flooding in the town of Old Fangak, from which Médecins Sans Frontières evacuated thousands. Humanitarians are responding to the urgent food and other basic needs of the flood-affected, but high floodwaters combined with insecurity are limiting their access and reach. Above-average rainfall is expected for the remainder of the rainy season through October, and the risk of additional flooding remains high. Overall, 2025 flooding is projected to be similar to or exceed 2024 levels, likely peaking in October.
While the burden of returnees and refugees from the Sudan war remains exceedingly high at over 1.2 million, cross-border migration has slowed in recent months. Between June and August, 19-23,000 people crossed each month, down from 30-47,000 per month January through March. Displacement dynamics have become increasingly fluid along the Sudan-South Sudan border amid shifting security and humanitarian conditions. Between April and September, the UN High Commissioner for Refugees (UNHCR) reported that over 199,000 people (130,000 Sudanese and 70,000 South Sudanese) fled South Sudan for areas of eastern Sudan that have recently become more secure, with the outflow driven by insecurity, limited humanitarian services, and reports of reduced food assistance. FEWS NET corroborated UNHCR’s report during a rapid field assessment to Joda, Gerger, and Chemmedi payams of Renk County (Upper Nile) in September, though FEWS NET also observed a continued inflow of Sudanese refugees fleeing insecurity in Sudan’s Blue Nile State. In addition, over 7,000 returnees remain at transit centers in Renk, with over 3,000 voluntarily relocated outside the transit center to engage in cultivation and other livelihood opportunities.
Displacement dynamics are also increasingly fluid across South Sudan’s other borders as humanitarian and economic conditions deteriorate in refugee settlements in neighboring Kenya and Uganda. Over 9,300 South Sudanese refugees returned from Kakuma camp in Kenya – most arriving in Torit (6,300) with some in Kapoeta East (660) – driven by 60 percent ration cuts and re-prioritization of beneficiaries that reportedly left 45 percent of South Sudanese refugees without assistance. Similarly, South Sudanese refugees in Uganda are reportedly facing ration cuts; however, persistent conflict and insecurity along the Uganda-South Sudan border are preventing spontaneous returns from Uganda to parts of Morobo, Yei, and Kajo-Keji counties of Central Equatoria through which returnees typically engage in crop production and other livelihood options.
South Sudan’s macroeconomic conditions remain poor amid ongoing uncertainty around oil production prospects and the persistent cash liquidity crisis. The intensification of fighting in Sudan’s Greater Kordofan region, coupled with recent drone attacks at Heglig oil processing facility in late August, are again threatening to disrupt South Sudan’s oil exports via Port Sudan. This is likely to affect hard currency inflows and sustain the depreciation of the SSP, which is trading at 6,100-6,200 SSP/USD on the parallel market and 4,628-4,638 SSP/USD on official markets as of mid-September. Although the month-on-month trend in the exchange rate remained stable on both the parallel and official markets in September, the SSP depreciated by 35 and 55 percent, respectively, compared to last September.
In early September, retail food prices remained elevated and financially inaccessible for many poor households who face persistently poor economic opportunities and low purchasing capacity. Compared to the same time last year and the five-year average, the price of red sorghum per malwa (3.5 kilograms) in Aweil Centre and Juba markets ranged between 117-164 percent higher and between 430-522 percent higher, respectively. Compared to last month, cereal prices have held steady despite an improvement in food supplies due to the arrival of local harvests and Ugandan imports. This stability in prices despite improved supply is primarily due to the depreciation of the SSP and high transportation and marketing costs.
Humanitarian food assistance remains crucial to ameliorating food consumption gaps, mitigating malnutrition, and saving lives, both among the South Sudanese population and Sudanese refugees. Based on WFP’s latest available distribution data, the agency provided food assistance to 1.5 million people in July, approximately 10 percent of the population. However, FEWS NET estimates needs are in the range of 8.0-8.99 million people or more. In 13 of the 40 counties where WFP is engaged in the lean season response, food assistance was considered significant (meeting at least 25 percent of the daily kilocalorie needs for at least 25 percent of each county’s population). However, sporadic conflict, persistent insecurity, and flooding continue to limit access in some areas of highest need, particularly in the Upper Nile and northern Jonglei border region. In Nasir and parts of Ulang, airdrops remain the only viable delivery option amid insecurity along the Sobat River.

Recommended citation: FEWS NET. South Sudan Key Message Update September 2025: Persistent conflict and flooding sustain a risk of Famine (IPC Phase 5) in Upper Nile, 2025.

This Key Message Update provides a high-level analysis of current acute food insecurity conditions and any changes to FEWS NET's latest projection of acute food insecurity outcomes in the specified geography. Learn more here.