Over a decade after independence and six years after the signing of the revitalized peace agreement, people in South Sudan continue to face critical humanitarian conditions. The humanitarian crisis has persisted due to a combination of sporadic armed clashes and intercommunal violence, food insecurity, public health challenges and climatic shocks. These factors have severely affected people’s livelihoods and hampered access to water, sanitation and hygiene (WASH), education and health services. In 2024, the economic crisis, the conflict in neighbouring Sudan and widespread flooding deepened people’s needs. Protection concerns remain high, especially for women and girls.
Climate variability
South Sudan ranks as the second most vulnerable country to natural hazards in the world, according to the 2024 INFORM Risk Index. South Sudan continues to experience extreme climate shocks such as floods, droughts and heat stresses that occur multiple times, giving communities no time to recover. The cumulative effects of climate change create a situation of perennial vulnerability of communities, wiping out local adaptive response mechanisms.
In 2024, heavy rains and the release of water from a historically full Lake Victoria in Uganda increased the levels of the Nile River – causing floods and affecting up to 1.4 million people as of mid-November 2024. These include communities who have yet to recover from the devastating floods between 2019 and 2022, which affected more than 1 million people each year. The prolonged flooding rendered basic needs such as food, clean water and health care difficult to access and contributed to the near collapse of local livelihoods. The areas most affected by the current floods are those already facing high levels of vulnerability due to previous flooding, conflict and the impact of the Sudan crisis.
According to the IGAD Climate Prediction and Application Centre East Africa Drought Watch of July 2024, drought silently affected all 10 states of South Sudan at varying extents – with its impacts unnoticed due to those of flooding. Nearly 36 per cent of the population is affected by different categories and impacts of drought-like situations, including induced displacements, which are forecasted to be much higher in 2025 due to the residual effects of El Niño. This is likely to cause more crop failure and food insecurity, with the need for more humanitarian support.
In March 2024, South Sudan experienced abnormally hot climate-induced weather conditions with temperatures reaching 45° C – above the normal average between 25° C and 35° C. The prolonged period of heatwaves increased the risk of human-related illnesses, particularly among children, the elderly and adults with underlying conditions, and affected socioeconomic conditions and people’s access to services.
Conflict
Conflict and insecurity continue to be significant drivers of people’s needs. Incidents of violence attributed to conventional parties to the conflict remained relatively low due to general compliance with the Revitalized Agreement on the Resolution of the Conflict in the Republic of South Sudan. However, entrenched patterns of violence involving armed youth, such as cattle raiding, border disputes and retaliatory attacks, are predominant drivers of violence.
Climate shocks affect different parts of the country at varying intensities, leading to multiple intercommunal conflicts at sub-national levels, including farmer-herder conflicts, cattle raids, land disputes and disputes over resources such as water. Flooding normally coincides with the cropping season in many parts of South Sudan or harvesting periods in places of early cropping, exacerbating food and nutrition insecurity. In several parts of the country, tensions between conflicting communities over access to resources and revenge have culminated into violent clashes and triggered serious human rights violations, including widespread sexual violence, particularly against women and girls.
During the second quarter of 2024, the United Nations Mission in South Sudan documented 1,062 victims of intercommunal and political violence, representing a 43 per cent increase in the number of incidents documented in the same period in 2023. According to the report, intercommunal violence involving community-based militias and/or civil defense groups, including cross-border conflicts, constituted the primary source of violence affecting civilians in South Sudan – accounting for 83 per cent of documented victims. Localized violence, exacerbated by long-standing cultural practices and communal tensions over access to natural resources, continues to be the major source of insecurity, posing access challenges for humanitarian operations and triggering population displacement across South Sudan.
Sudan crisis
Since the conflict erupted between the Government of Sudan Armed Forces and the Rapid Support Forces in Sudan on 15 April 2023, over 874,000 people have been recorded crossing into South Sudan as of the end of November 2024 – with an additional 342,000 people expected to arrive in 2025. People fleeing Sudan face extreme protection risks along treacherous routes to South Sudan, with many – especially women and girls – exposed to violence and gender-based abuse and arriving in poor physical and psychological conditions. Urgent life-saving assistance remains critical, including food, nutrition, shelter and WASH services, health and vulnerability screening, vaccinations for children, and mental health and psychosocial support (MHPSS).
The sheer volume of arrivals is overwhelming South Sudan’s limited infrastructure, particularly in border areas where congestion in transit centres heightens protection, gender-based violence (GBV) and health risks. Transportation constraints and the strained capacity of host communities underscore the need for increased support to move people quickly to safer locations. For those who reach their destinations, reintegration poses severe challenges. Returnees face crippling food insecurity in communities already affected by floods and economic hardships. Access to health care and education is vastly limited, compounded by the scarcity of facilities, personnel and supplies. Many returnees lack civil documentation, affecting their access to basic rights and services. Land ownership and eviction issues further complicate access to secure, affordable housing, with prohibitive land costs making stability a distant goal.
The Sudan crisis compounds South Sudan’s humanitarian emergency, demanding an urgent expansion of response capacities. Returnees are arriving in areas already grappling with service deficits and strained community resilience. Meanwhile, the conflict has destabilized markets in border states, causing prices of food and essential commodities to skyrocket, and heightening risks of secondary displacement to collective sites and urban centres. Onward movements from border points to transit centres and final destinations remain vital. Transit centres require immediate expansion and maintenance to accommodate and provide safe places for new arrivals. In high-return areas, a major scale-up of services is critical, especially for health care and education, to support host communities already absorbing internally displaced persons (IDPs) and returnees. To prevent prolonged dependency on humanitarian aid, enhanced livelihood programmes and addressing housing, land and property (HLP) issues are essential to help returnees achieve self-sufficiency upon arrival.
Disease outbreaks
South Sudan is home to multiple public health crises, exacerbated by limited immunization coverage, disruptions in vaccination services, widespread population displacement, influx of displaced people from Sudan and poor household nutrition. Inadequate access to safe drinking water and sanitation and natural disasters such as floods increase the vulnerabilities of communities, posing additional challenges to public health emergencies. South Sudan faces significant gaps in timely detection, reporting, investigation and response to disease outbreaks. The public health system is fragile and dependent on humanitarian aid. The Government’s funding for health remains significantly low at 2 per cent of the national budget.
People in South Sudan continue to experience diseases, with people in some areas enduring multiple outbreaks simultaneously – intensifying the burden on communities and the health system. There are 19 of 20 neglected tropical diseases in South Sudan, highlighting the health service challenges in the country. It is estimated that only 44 per cent of the population live within reach of health facilities with consistent access to primary care services. The available health facilities are poorly equipped and staffed. Vaccine-preventable disease burden looms large due to limited coverage in immunization programmes, with many children and adults vulnerable to diseases including measles, yellow fever and poliovirus. Years of flooding continue to drive the upsurge of endemic diseases such as malaria, with the peak season extending from July to December. Malaria remains a leading cause of morbidity and mortality nationwide, accounting for 47 per cent of overall morbidity. Since January 2024, 2.7 million suspected cases of malaria and 1,800 suspected malaria-related deaths have been recorded.
1.1 Crisis overview
1.2 Analysis of shocks, risks and humanitarian needs
Confluence of shocks drive humanitarian needs
Multiple shocks have had a devastating impact on the people of South Sudan. Approximately 9.3 million people or 69 per cent of the country’s 13.4 million population will require some form of humanitarian assistance in 2025. The outlook for 2025 is difficult, with several factors compounding pre-existing vulnerabilities such as high malnutrition rates, the impact of the Sudan crisis on South Sudan, severe flooding, an unprecedented economic crisis and insufficient government services. As of the end of November 2024, the war in Sudan has resulted in over 877,000 returnees, refugees and asylum-seekers crossing into South Sudan. The war cut oil exports, denying critical revenue to South Sudan. The local currency has sharply depreciated, government workers have not been paid for months, and the Sudan crisis has disrupted trade and drove up food prices and the cost of living. In October 2024, South Sudan’s first cases of cholera were confirmed to have arrived from Sudan. Floods have increased the risk of disease outbreaks, disrupted health services, destroyed infrastructure, washed away crops and damaged safe water facilities, schools and other services.
A protracted humanitarian crisis
Since 2015, the estimated number of people to need some form of humanitarian assistance has increased from 6.4 million to 9.3 million in 2025 – nearly three-quarters of South Sudan’s population of 13.4 million. Approximately 6.3 million people are severely food-insecure in the Integrated Food Security Phase Classification (IPC) Phase 3+, with the number projected to increase to 7.7 million people in the 2025 lean season between April and July. Two million people remain displaced due to decades of conflict, intercommunal violence and the impacts of climate events. Most of the displaced are within host communities, further straining limited resources and essential services. The root causes of displacement have not been effectively addressed, which undermines the collective ability to provide pathways to solutions and compound the lack of livelihood opportunities for displaced people – contributing to over-reliance on humanitarian assistance.
South Sudan continues to face difficult macroeconomic challenges, partly resulting from the spillovers of the war in Sudan. The country faces a severe economic crisis characterized by a significant drop in state revenue, depreciating local currency, high inflation rates and widespread poverty. As South Sudan's economic situation worsens, living costs continue to soar nationwide.1 The Cash Working Group (CWG) and REACH’s Joint Market Monitoring Initiative (JMMI) data reveals that the cost of a household minimum expenditure basket increased by 250 per cent between February to September 2024. Most monitored markets operated with limited functionality between September 2023 and August 2024, facing issues with accessibility, affordability and availability of goods, and supply chain resilience and infrastructure.2
High levels of food insecurity
South Sudan is one of the top five of 18 globally identified hunger hotspots3, with high levels of food insecurity due to multiple shocks such as flooding, insecurity, displacement and inflated cost of living. From December 2024 to March 2025, an estimated 6 million people or 45 per cent of the population will likely face crisis level of food insecurity (IPC Phase 3+), with Unity, Jonglei and Upper Nile states the most affected. This number will rise during the lean season (April-July 2025) to an estimated 7.7 million people or 57 per cent of the population across Unity, Upper Nile, Jonglei, Northern Bahr el Ghazal, Warrap, Lakes and Central Equatoria states. Meanwhile, 85 per cent of South Sudanese returnees from Sudan are likely to experience crisis levels or worse food insecurity conditions (IPC Phase 3+).
Key drivers of food insecurity in South Sudan are economic crisis, insecurity, extreme climate events, intercommunal conflict, the impact of the Sudan crisis, low agricultural production and reduced household coping capacity to shocks. The situation is exacerbated by the persistent multisectoral humanitarian needs and access constraints that hamper food delivery. The effects of the 2024 flooding are expected to extend into 2025 as crop production is projected to decline, particularly in the hardest flood-hit areas. Road damage will further disrupt agriculture and markets, decreasing livestock resilience and increasing food insecurity as households face limited purchasing power.
The high levels of food insecurity and other compounding factors have led to alarmingly high levels of acute malnutrition. The 2024 Food Security and Nutrition Monitoring System (FSNMS) and other Standardized Monitoring and Assessment of Relief and Transitions (SMART) surveys estimate 2.08 million children under age 5 at risk of acute malnutrition in 2025, a 26 per cent increase from the projection in 2024. The surveys also suggest that 650,000 children under age 5 will be at risk of severe acute malnutrition in 2025, a 33 per cent increase from the 2024 estimates. An estimated 1.1 million pregnant and lactating women (PLW) will need life-saving treatment for acute malnutrition in 2025.
Community priorities
From September 2023 to October 2024, partners carried out consultations with selected communities in Unity, Upper Nile and Jonglei states, who identified food security/livelihood support, health care, children’s education, flood mitigation and security as top priorities.
In Unity State, communities noted food security as a top priority, as insecurity aggravated by a lack of food and restricted livelihoods due to flooding prevent people from returning. Communities expressed the need to produce their own food and requested the timely distribution of seeds, agricultural tools and equipment, fishing kits, canoes and beekeeping kits. In Guit Town, community members proposed using the existing 33 community groups to create cooperatives focusing on agriculture, fishing, health and sanitation projects.
In Upper Nile State, livelihoods were a top priority for the communities, who requested land for farming, timely distribution of seeds, tools, machinery, pesticides and training on its use. In several communities, male members also expressed interest in masonry, bricklaying, electrical work and tailoring, while women welcomed finance initiatives to start small businesses.
In Jonglei State, communities mentioned food security as a top priority. While some requests were made for short-term food assistance, most community members expressed the need for land to farm and grow their own food, as well as seeds, farming and fishing tools, canoes, training in agronomic practices and animal restocking.
Read more in Part 6: Community priorities
1.3 Humanitarian outlook & risks
Humanitarian outlook & risks
As the world’s second most vulnerable country to natural hazards, South Sudan will continue to be affected by extreme effects of climate variability – flooding in some areas and drought in other areas. Between 2019 and 2022, floods affected over 1 million people each year, mainly in the north and northeastern parts of the country. Back-to-back drought-like conditions have severely affected communities in the southeast since 2020, particularly in Eastern Equatoria. These climatic variabilities will continue to affect communities in 2025 and beyond.
With no solution found for the Sudan crisis, South Sudan will remain vulnerable to its impact. As of mid-December 2024, more than 904,000 people have been recorded arriving from Sudan. Projections indicate an additional 337,000 arrivals expected in 2025. Large numbers could arrive in South Sudan in the event the conflict shifts closer to the border or the humanitarian situation in Sudan deteriorates further.
The Sudan crisis will continue to affect the economic situation in South Sudan, inflating the cost of essential commodities and pushing communities – whose coping capacities have already been exhausted – to further deprivations. Overall, the rising cost of food and fuel will make the cost of basic items unaffordable for many people in South Sudan, who will need some form of humanitarian assistance to cope with the situation.
Floods, the influx of arrivals from Sudan, cholera and the threat of diseases in neighboring countries (e.g., mpox, Marburg etc.) will increase the vulnerability of epidemic outbreaks in South Sudan, which will further stretch the fragile health care system.
The timeline of events and season of events
The digital version of the timeline of events and season of events can be found at: Humanitarian Action (bit.ly/3OBVir9)
