Armed clashes took in Wau State from late June 2016 to January 2019 between the Dinka-dominated Sudan People's Liberation Army (SPLA) and local opposition forces, consisting of tribal Fertit militias as well as fighters claiming allegiance to Riek Machar. It is unclear to what extent these rebels were actually part of the SPLM-IO or acting independently while using the SPLM-IO's name. The clashes resulted in the arrest of the state's governor, Elias Waya Nyipuoc, widespread death and destruction in the state capital, Wau town, and the displacement of up to 150,000 people.

Background Rivalries and violence between various ethnic groups have a long history in South Sudan. Many minorities in the country believe that their communities are threatened and marginalized by the Dinka people who have traditionally dominated the administration of southern Sudan. The Fertit are one such minority, and mostly concentrated in areas of former Western Bahr el Ghazal, including Wau State. The animosity between Dinka and Fertit became deeply entrenched during the Second Sudanese Civil War, when the Dinka-dominated Sudan People's Liberation Army (SPLA) waged a rebellion against the Sudanese government. Many Fertit opted to stay loyal to Sudan or remain neutral, as they feared suppression at the hands of the Dinka in an independent South Sudan. The SPLA responded by attacking Fertit as perceived enemies of the rebellion, causing militant Fertit to organize the so-called Army of Peace in self-defense. This militia then became involved in widespread massacres of Dinka from 1986, worsening ethnic relations even further.

Increasing violence in Wau State

In 2015, the South Sudanese government and the SPLM-IO signed the ARCSS peace deal in an attempt to end the civil war. Both sides used concessions in the agreement to their advantage, however, and the agreement gradually fell apart. Wau State was an area which was affected by the ARCSS. The SPLM-IO mobilized forces in Wau, and then demanded that these rebels were granted cantonment zones and be included in the ARCSS' security provisions. This was unacceptable to Gen. Paul Malong Awan, the SPLA's chief of staff, who responded by mobilizing loyal army elements such as Mathiang Anyoor units. He then circumvented the formal chain of command, and ordered these SPLA troops to crush the opposition by force, even though the peace agreement was still in force. This resulted in growing ethnic tensions in Wau State from early December 2015. The SPLA soldiers deployed to the region for counter-insurgency operations mostly belonged to tribes from Northern Bahr el Ghazal and Warrap, while the local SPLM-IO fighters intensified their operations.

On 2 December, the SPLM-IO reportedly attacked government units at Busseri and Firka, causing the SPLA to send reinforcements to these area, which were in turn ambushed and defeated by the rebels. Three days later, clashes between rebel and government fighters broke out around Bisellia, Bazia, Faraj Allah, Bringi, Mapel, and the Bo River Post. Amid the fighting there were reports that the Ugandan People's Defence Air Force and/or the South Sudan Air Force conducted aerial attacks against both rebel as well as civilian targets using attack helicopters. The UNO consequently criticised the SPLA for breaching the national ceasefire by conducting offensive operations.

At the same time, Human Rights Watch reported that the newly deployed government soldiers, mostly Dinka, began to abuse the local Fertit population, forcing tens of thousands to flee Wau. Many civilians were arrested and then murdered as purported SPLM-IO supporters. Governor Elias Waya Nyipuoc admitted that by 30 May 2016, he had confirmed that at least 100 civilians had been murdered by SPLA soldiers, and had reported the cases to the government. Unable to stop them, he said that the soldiers probably abused the local population because the government had failed to pay or feed them. This caused them to rob what they needed. Waya argued that this behavior was to be expected when the government neglected their military forces. The SPLA leadership, meanwhile, denied that any abuses at the hands of SPLA soldiers had taken place in Wau. In addition to the violence of the SPLA against civilians, no progress was made in the attempts to enforce the ceasefire between the SPLA and local SPLM-IO groups, as the government denied that the SPLM-IO had any presence in the whole Bahr el Ghazal region to which Wau State belongs. As result, no agreement for SPLM-IO cantonment areas in Wau State was reached. On 9 April, the SPLA command even announced that they would launch an offensive in Bahr el Ghazal and Equatoria to destroy all SPLM-IO units in these regions.

At the same time, the SPLA soldiers were accused by the opposition of intensifying their abuses of Fertit civilians, while reportedly working together with local Dinka militants and armed cattle herders in their attacks. The violence in Wau further increased in June, as individual Fertit began to fight back by murdering soldiers, policemen and Dinkas. This in turn caused revenge killings by Dinkas and SPLA against Fertit. In addition, insecurity in the state increased dramatically, as local SPLM-IO and SPLA units ignored the ceasefire and clashed on several occasions at Bagari and Angu Angu. At least 8 SPLA soldiers were killed, while Raga town in the neighbouring Lol State was overrun by rebels for a short time, resulting in the death of several bodyguards of the local governor.

Clashes Battle in Wau town

By 23 June, a larger battle south of the state capital, Wau town, broke out between SPLA and SPLM-IO, the latter claiming to fight in order to protect the local Fertit people from attacks by the Dinka-dominated SPLA. As result of the increasing violence, a state of emergency was declared in Wau town, and the SPLA's 5th Division moved in, officially to prevent further escalation of violence. These forces were under the command of Lt. Gen. Gabriel Jok Riak, who had been accused of human rights abuses by the United Nations during the South Sudanese Civil War. Governor Waya initially claimed to support the emergency declaration, stating "All who are here are rebels, so the Division [5 of the] SPLA is ready and even those who are just walking around are ready". However, opposition groups claimed that the army soon began to plunder the state capital, and to assault the civilian population, leading Governor Waya to criticise the soldiers. On 24 June 2016, President Kiir unexpectedly sacked Waya, and just a few hours later, had him arrested. A local SPLA commander declared that Waya had been arrested because he was responsible for the deteriorating situation in the state, claiming that he had no respect for the military and talked "nonsense". A few days later, a document began to circulate on the internet that claimed that Lt. Gen. Mangar Buong Aluenge of the SPLA had plotted from the very beginning to remove and arrest Waya, while the Society for Threatened Peoples believed that Waya's criticism of the army had led to his arrest.

As result of Waya's dismissal, the situation escalated completely, as a heavy battle broke out in Wau town on evening of 24 June. Dinka youth militants in civilian clothing and uniforms entered Wau's south-western neighbourhoods, where they murdered and raped Fertit civilians. According to independent and opposition sources, as army soldiers and Dinka militias intensified their attacks on the town's Fertit population, many locals picked up arms and began to fight the pro-government forces. They were supported by armed Fertit youth from the countryside, who also came into Wau town to take revenge against the Dinkas. The SPLM-IO claimed that their forces had stayed out of Wau town, but attacked SPLA soldiers to protect Fertit civilians in the settlement's southern outskirts. Massacres continued throughout the night, but by late 25 June the SPLA claimed to have secured the town and began to search for hiding insurgents. The army imposed a curfew in Wau town the next day, and, according to local civilians, together with Dinka tribal fighters once again began to kill, rape and rob the local Fertit civilians. These began to flee en masse to the nearby UNMISS base and local churches for protection; others escaped to areas held by SPLM-IO-aligned Fertit militias such as the "Fertit Lions". The government forces, however, maintained that the whole battle was the result of tribal fighters invading the town, whereupon "some greedy civilians started immediately on a looting spree". Accordingly, the army had just defended itself and not preyed on civilians, though army spokesman Lul Rurai Koang said that it was possible that individual soldiers might have participated in the looting.

On 28 June, Wau town was once again attacked by a major force of insurgents, reportedly 350–700 fighters. Independent and opposition sources claim that the assailants belonged to a pro-Fertit, SPLM-IO-linked tribal militia, while the government said they were part of the "Islamic Movement for Liberation of Raja". This group, government spokesman Makuei Lueth further claimed, wanted establish an Islamic state in the region, but also included members of the Christian Lord's Resistance Army. He accused Sudan of backing them. The assault was eventually repelled, and afterwards Dinka gunmen once again began to loot the town and executed anyone opposing them. While the government claimed that the looters were unrelated criminals, locals believed them to be SPLA soldiers as they wore uniforms. UNMISS also said that a total breakdown of law and order had taken place in Wau. A least 30 people were killed while attempting to protect the properties of civilians who fled their homes. After the attackers were driven off, the pro-government mayor of Wau town quickly declared that the town was safe again, but most residents refused to return home. One civilian stated that "Up to now, people are not really secure because some of the soldiers are still moving around."

Meanwhile, the official SPLM-IO leadership attempted to distance itself from the local uprising. It was estimated that the fighting in the Wau State had resulted in over 400 civilians killed, and up to 120,000 displaced. Of these, 12,000 had sought refuge in the local UNMISS base.

On 2 July, the new Governor of Wau, Andrea Mayan, declared that the situation in the state capital had been stabilized, with people being able to return home. A high level committee had been formed to investigate the clashes, and the curfew was lifted. The Guardian, however, reported that by 5 July, only the Dinka-dominated parts of Wau town "were lively. Pick-up trucks mounted with machine guns and full of soldiers toting AK-47s, mostly Dinka, patrolled the area. In contrast, the southern and western parts of town, home to the Fartit, were deserted after people flocked to churches and the UN base for protection."

On 7 July, another battle broke out in Wau town, resulting once again in a civilian mass exodus. By then, it was estimated that 150,000 people had fled Wau town, leaving it mostly deserted. Malaria had broken out among the refugees, most of which were forced to live in the bush. Government and rebel forces blamed each other for the renewed fighting; SPLM-IO Maj. Gen. Ashhab Khamis Fahal Ukanda stated that "They [the government] don't think other people have rights in this country. We all worked together to bring independence of the country. But they have turned against the rest of the people. They think they are born to rule. We will not accept that." Three day later, sporadic, small-scale clashes broke out among SPLA units in Wau town.

Fighting in the countryside