For the war refugees who have escaped ransacked South Sudanese towns and impoverished villages, and for the aid workers assisting them in the western Ethiopian region of Gambella, now is a time for waiting.

Mary Ban, 26, has been stuck in a camp on the Ethiopian border during the rainy season, sleeping in a large communal tent with her four children. They’ve got no mosquito nets or sheets, and she’s not happy with the grain distributed by the UN as it causes diarrhoea. But because the Tierkedi and Kule camps are full, and Leitchuor camp flooded, she will have to remain in Pagak for a while.

“I am waiting to be relocated,” she says, pausing from bundling firewood to sell. “We will be here until we [are] taken to the place we need.”

The uncertainty in the refugee operation is twofold. Though a difficult situation is under control for now, many believe heavy fighting will resume in South Sudan once roads dry up, leading to a new surge of tens of thousands of refugees. Moreover, Ethiopia’s government is struggling to find suitable locations for flooded refugees and potential new arrivals that do not disturb volatile local political dynamics.

Ban, an ethnic Nuer from Mathiang in Upper Nile state, has been offered space at a camp along with 3,000 other people at Pagak. Only 12 accepted. That is because the camp is more than 250 miles away, in the south of Gambella – far from the Nuer strongholds in the region and close to their ethnic rivals, the Dinka.

“We need to be in Kule, but we don’t want another area. We don’t like Dima, as it’s near to the Dinka side. Dinka came to Mathiang and killed a lot of people; children, women and old people,” she said.

Ban is one of almost 200,000 primarily Nuer refugees who have ended up in Ethiopia since December 2013, when attempts by Kiir to arrest political rivals for coup plotting – including his Nuer former deputy, Riek Machar – prompted commanders to rebel. The ensuing clashes have claimed thousands of lives and displaced nearly 2 million people (pdf).

Ceasefire deals have been signed in Addis Ababa, but in reality it is the rainy season that has discouraged the movement of potential refugees and armed groups. The result has been a huge reduction in people crossing the border, despite severe food shortages inside South Sudan.

Aid organisations nonetheless remain alert: fading rains could lead to renewed fighting, causing a surge comparable to the first few months of the crisis, when thousands a day were arriving.

“That’s why humanitarian agencies are working with a 100,000-extra influx in the latest months of the year,” explains Dennis Solberg Kjeldsen, regional operations coordinator for the International Federation of Red Cross and Red Crescent Societies. “So right now there’s a little bit of a lull … but we’re quite sure we’re going to need the resources, we’re going to need funding.”

Funds are in heavy demand because of the exceptional number of emergencies occurring globally, not least the Ebola outbreak. “I don’t want to underestimate or downplay the threat of Ebola, but Ebola has taken an enormous amount of attention away from ongoing emergencies on the continent,” he said. The UN refugee agency has received 37% of the requested $567m (£355m) needed to deal with the 2 million displaced inside and outside South Sudan.

Aid workers are also waiting for Ethiopia’s federal and regional governments to settle on an alternative to the existing Okugu camp near Dima.

Aside from the refugees’ fears regarding the Dinka, there are tensions in Gambella (pdf) between the Nuer and the Anuak people, another Nilotic ethnicity, which complicate the decision. Although Gambella is one of Ethiopia’s most sparsely populated areas, access to its plentiful land and water is contested. Because of its fertility, the federal government hasearmarked the state for commercial agriculture.

The Anuak, who consider themselves the original inhabitants of the area, feel encroached upon by the now more populous Nuer, and also threatened by foreign and highland farming investors. This year’s influx of Nuer – equal to 60% of Gambella’s 2007 official population of 307,000 – is only the latest instalment in a century-old trend. The rate of arrival has increased in the five decades since the southern Sudanese began their struggle against Khartoum.

Anuak discontent manifests itself in sporadic violent clashes, most recently with highlanders. In 2012, Anuak rebels killed workers at a prominent rice farm, leading to reprisals by security forces. A scuffle between schoolchildren this month led to a series of tit-for-tat killings and mob violence between Anuak and highland communities in Abobo and Gambella towns, according to Anuak elders and local security sources. The scars of a 2003 bout of violence – when, according to Human Rights Watch, soldiers and militias targeted Anuak civilians after acts of banditry – have barely healed. Anuak people fear a repeat of what some call a massacre.

There is also resentment at the arrivals from the west. One of the Anuak elders, Ochodo Obang, sees all Nuer settlers as foreign colonisers. “These people are like the highlanders; they want to take our land. We are the owners of the land.

“We don’t want them to be here at all. It’s not a question of do we put them here or there.”

The problem for officials is how to accommodate tens (and possibly hundreds) of thousands more Nuer in the next few months without stoking disputes. The dry and stable Kule and Tierkedi camps that house about 100,000 people are in former Anuak areas, Ochodo says. The ill-fated government decision to choose Leitchuor camp – located in a floodplain, it is now largely submerged – resulted from a lack of good options.

“There’s a lot of difficult issues around it, not least the ethnic dimensions,” said Kjeldsen of the government’s choice. “We have to be careful we don’t exacerbate any tension.”