South Sudan: Humanitarian Snapshot (September 2025)

In September, communities across South Sudan continued to face severe humanitarian challenges, including flooding, food insecurity, violence, displacement, and disease outbreaks. As of 30 September, over 639,000* people were affected by flooding in 26 counties across six states, with Jonglei and Unity worst hit. The number is expected to rise as rains persist, and assessments continue. Floods have damaged homes, crops, schools, boreholes, and other public infrastructure. Many roads remain impassable, hampering access to affected populations. In Upper Nile (Ulang, Nasir, Baliet), Jonglei (Fangak), and Unity (Panyijiar), the food security situation is worsening. Humanitarian partners have endorsed a multi-sectoral response plan targeting 300,000 people to prevent deterioration into catastrophic food insecurity. Conflict and insecurity, particularly in Upper Nile, Jonglei, Central Equatoria, and Western Equatoria, have also triggered mass displacement. Between January and September 2025, over 497,000 people were newly displaced, 321,000 due to conflict and 175,000 due to flooding. Recent clashes in Western Equatoria have displaced tens of thousands according to authorities. In Nagero County, nearly 21,000 people fled to nearby villages (as of 29 September). In Tambura County, over 10,000 people remain displaced. In Mundri East County, an estimated 30,000 people fled into the bush following fighting in Kediba Payam. The violence has resulted in significant civilian casualties and destruction of critical infrastructure, including health facilities, schools, and public buildings. Humanitarian access remains severely constrained by ongoing insecurity. Several disease outbreaks continue to affect communities including Anthrax (Jur River, Gogrial West), cVDPV2 (Yambio, Juba, Ayod), Hepatitis E (Fangak, Renk), Mpox (Juba), and Cholera. A cumulative 93,200 cholera cases, including 1,565 deaths, were reported across 55 counties in nine states and three administrative areas.