South Sudan's Return to War: How NGOs and UN Agencies Can Safeguard WASH Operations During Active Conflict

By Specialized Logistics Solutions | Updated March 2026 | Download the SLS Product Catalogue

Since late December 2025, renewed fighting between the South Sudan People's Defence Forces (SSPDF) and opposition forces has swept through Jonglei and Upper Nile states — two of the country's most conflict-prone and flood-prone regions. In a matter of weeks, more than 280,000 people have been displaced, health facilities have been looted, and cholera treatment centres have been overwhelmed. The UN Emergency Relief Coordinator has called it a "perfect storm" of conflict, climate shocks, and deprivation. For humanitarian organisations operating in South Sudan, the question is no longer whether a crisis is coming — it is already here.

For NGOs, UN agencies, and implementing partners, the ability to maintain Water, Sanitation, and Hygiene (WASH) operations during active conflict depends on one thing above everything else: pre-positioned supplies and a reliable last-mile logistics partner already inside the country.

The Scale of the Current Crisis

According to OCHA's latest Flash Update, clashes across Uror, Nyirol, Akobo, Duk, Ayod, and Canal/Pigi counties are producing daily civilian casualties and fresh waves of displacement. Fighting has reached within 100 kilometres of Juba. Aid convoys have been looted and three humanitarian workers were killed between February 7–16, 2026 alone.

"Here in South Sudan, you have this perfect storm of climate change and conflict and inequality and poverty." — Tom Fletcher, UN Emergency Relief Coordinator, February 2026

The cholera situation is particularly alarming. Since September 2024, South Sudan has recorded 97,801 cholera cases and 1,608 deaths across 55 counties in nine states. January 2026 alone saw 479 new cases nationwide, with cholera treatment centres in Jonglei described by OCHA as "critically short of supplies." Meanwhile, WHO projects that 6.3 million people will require health assistance in 2026, driven by flooding, disease outbreaks, and supply chain disruption.

The approaching rainy season — beginning in March — will compound every one of these pressures. Roads in Jonglei become impassable. Air access becomes the only lifeline. And in communities sheltering in schools, churches, and open bush with no sanitation infrastructure, the risk of waterborne disease reaches critical levels.

Why WASH Supply Chains Break Down in Conflict Zones

Conflict disrupts WASH operations in three interconnected ways that humanitarian planners must account for before violence escalates:

•Road access collapses. Frontlines cut the main supply routes to affected counties. In Jonglei, road access to northern and central areas was already severely restricted by February 2026.

• Storage infrastructure is looted or damaged. Multiple aid agencies, including Oxfam, had facilities looted and staff displaced in January and February 2026, suspending services to over 400,000 people.

• Procurement lead times become critical. Ordering water purification tablets or dewatering pumps from international suppliers takes weeks. When cholera spreads in a displacement camp, you have days.

The only reliable mitigation is pre-positioning. Organisations that had critical WASH stocks inside South Sudan before the fighting escalated were able to continue responding. Those that did not were forced to suspend operations or wait for supply windows that may not come.

Critical WASH Equipment for Active-Conflict Response

Based on SLS's operational experience responding to South Sudan's cholera emergencies — including our documented responses with P&G Purifier of Water and Aquatabs — the following equipment categories are essential for any rapid WASH deployment in a conflict-affected area:

•        Water purification at point of use. P&G Purifier of Water sachets and Aquatabs chlorine tablets are the fastest deployable treatment solutions for displaced populations with no access to treatment infrastructure. Each sachet treats 10 litres and requires no equipment or technical training.

•        Flexible water storage. Butyl Products onion bladders and Oxfam-standard steel tanks — available through SLS's WASH product range — allow rapid deployment of safe storage capacity at IDP sites and health facilities.

•        Dewatering and submersible pumps. Multiquip and Aussie pump systems are critical for both flood control at displacement sites and for drawing groundwater in areas where surface water is contaminated by conflict or flooding. See our full pump equipment range.

•        Modular warehousing for forward staging. Pre-positioning critical supplies requires secure, deployable storage at accessible points inside affected states — particularly given the high risk of looting. Hallgruppen modular structures, available through SLS, can be established quickly at humanitarian hubs without permanent infrastructure.

Procurement Recommendations for 2026

IOM issued a critical warning on 19 March 2026: nearly 187,000 displaced people in Bentiu and Malakal face collapse of clean water and sanitation services due to a $6 million funding shortfall. Without intervention, taps will run dry and sections of Bentiu camp will flood when the rains arrive.

For NGO and UN procurement teams, this is the planning window that determines operational capacity through July 2026. SLS recommends the following timeline:

•        March–April: Pre-position water purification stocks (P&G sachets, Aquatabs) and pump equipment at Juba and Malakal staging points before roads become impassable.

•        April–May: Deploy water storage capacity (onion bladders, Oxfam tanks) at IDP sites in Jonglei and Unity states ahead of peak flooding.

•        Ongoing: Maintain a rolling NFI stock — hygiene kits, shelter materials — at forward positions to enable same-week response to new displacement events.

SLS maintains pre-positioned stock in Juba and Kampala and can respond to emergency procurement requests with short lead times. Our team has 35 years of operational experience in South Sudan's most challenging environments, and we have delivered critical supplies for IOM, UNMISS, and WHO across multiple crisis cycles.

Operating Where Others Cannot

South Sudan's current crisis does not follow a predictable escalation curve. The combination of active conflict, a nationwide cholera outbreak, approaching floods, and reduced humanitarian funding from the USAID withdrawal creates an operating environment where supply chain failure has direct, measurable consequences for human survival.

The organisations that will continue to deliver results are those with trusted local partners, pre-positioned stocks, and logistics expertise that is not dependent on ideal conditions. If your organisation is planning its WASH response for the 2026 rainy season — or is already responding to the Jonglei crisis — contact SLS for a quote and availability check. We are operational, pre-positioned, and ready.

About Specialized Logistics Solutions

SLS is a Juba-based humanitarian logistics and WASH supplier serving UN agencies, NGOs, and government organisations across East and Central Africa. We are authorised distributors for Butyl Products UK, Multiquip, Aussie Pumps, and Hallgruppen modular structures. View our full product range →

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