Aid agencies say water and food provision has improved in four camps housing more than 105,000 refugees from Sudan's Blue Nile State, but flooding, disease and an influx of additional refugees pose new threats.
Two new camps have been set up in South Sudan's Upper Nile State to ease the strain on facilities in Jammam camp, which is suffering myriad health problems associated with recent floods.
"The conditions here in Gendrassa [camp] are okay, [though] there is still a lot of malaria. In Jammam, there is still a lot of diarrhoea. Here, we have some control over it," said Sheikh Abdel-Aziz Fadul, a refugee.
Stanlake Samkange, East and Central Africa director for the UN World Food Programme (WFP), expects more inflows into the camps as routes currently blocked by floods dry up.
"We are certainly planning for up to 30,000 more people coming in 2012. But there are many more people on the other side of the border than that," he told IRIN.
"My biggest concern is that if this number increases significantly, then it will put additional pressure on our efforts," he added.
Sudan's government forces and rebels have been fighting in Blue Nile State since September 2011, sending refugees south.
The number of incoming refugees tapered when rains, starting in April, began to cut off access to the camps. George Okoth-Obbo, Africa director for the UN Refugee Agency (UNHCR), thinks the number of refugees in camps in Upper Nile's Maban County and neighbouring Unity State, which currently have more than 60,000 refugees from Sudan's South Kordofan State, could soon swell again.
"When we were up in Maban and talking to the refugees, all of them were telling us this or confirming it… saying 'at least half my family is [still] in Blue Nile' and so on," he added.
Having planned, before the rains, for a maximum of 100,000 people in Upper Nile and Unity, the UN has had to dig into backup funds to fly in goods for shelter, cooking and sanitation for 170,000 people, while WFP is resorting to costly food airdrops.
"We cannot risk having gaps, and the airdrops are to fill the gaps," said Samkange.
Meanwhile, efforts to lift Sudan's block on aid to people stuck in South Kordofan and Blue Nile have yet to bear fruit. "The government in Khartoum agreed in principle that humanitarian access should be provided but we are still negotiating...about the terms," he said.
Pilar Bauza, UNHCR’s emergency health coordinator, says refugees have suffered respiratory and diarrheal diseases, malaria and malnutrition from poor living conditions and nutrition.
"These people were walking for about a month. They were in Blue Nile with no proper health system, and then they got even more vulnerable along the way," she said.
While aid agencies say they have been vigilant about addressing potential cholera outbreaks, the Jamam, Yusif Batil and Gendrassa camps in Upper Nile have been hit by an outbreak of hepatitis E. The disease results from consuming contaminated water.
"To date, a total of 384 suspected and confirmed hepatitis E cases and 16 deaths have been reported from the three refugee camps," since July, said a 13 September statement by the Ministry of Health.
Health education campaigns, an increase in water provision from 10 to 13 litres per day, and a drop in malnutrition from 40 to 33 percent have improved the health of the refugees, but more needs to be done.
"We are not out of the woods yet - this is not mission accomplished," UNHCR's Okoth-Obbo said. "There is still a lot ahead of us in terms of the condition of the people. We still have an unacceptably high level of morbidity. We need to bring down mortality."
Running out of money
Another key aim is to improve roads, which, after recent flooding, once again cut off access between Yusif Batil and Gendrassa camps.
But to continue providing basic services by the end of the year, UNHCR says it urgently requires US$20 million, having only received 40 percent of its $183 million appeal to manage humanitarian needs in the camps.
WFP says it has only received about a third of the $6 million it needs to airdrop food to the current caseload until the end of the year.
Compounding these issues is security.
UNHCR has long tried to move people away from Yida camp, considered too close to the border. "We did not think the location of Yida was viable - so close to the border, so close to the violence," Okoth-Obbo said.
Aid agencies also fear that armed groups are operating and recruiting refugees within camps in Upper Nile, as another deadline for Sudan and South Sudan to find a deal on the largely undefined border approaches.
"You can hear the shots come from over there, over there, over there and over there," said Sheikh Abdel-Aziz Fadul, a refugee, pointing to a sea of tents in each direction.