Nyayiel Kuony Tet watches the shower of fat white sacks as they tumble from the tail of a Hercules, seesaw through the sky and hit the earth with the crack of exploding fireworks.

The bags, each stamped with the logo of the International Committee of the Red Cross (ICRC), leave craters almost a foot deep in the green and marshy ground of Leer county.

Three months ago, Kuony Tet and many of the hundreds of people queuing patiently for the airdropped rations of sorghum, beans, salt and sugar were hiding in swamps and surviving on water lilies, roots and wild fruit.

Forced from their homes by the fighting that erupted in December, they grabbed what they could and fled to the bush to escape the conflict that has brought the world’s youngest state to its knees.

By January, the fighting had reached the predominantly Nuer Leer, leaving Kuony Tet and her 10 children with no choice but to run. But not all of them made it to the sanctuary of the swamps. Her 23-year-old son, Latjor, who had supported the family by fishing and tending their few cows, died while attempting to flee. “I heard a gunshot, but I could not run back,” Kuony Tet says. “We did not have time to bury him.”

She points to her neck, which, unlike that of most Nuer women, is unadorned. “When he was killed, I took off my necklace and threw it away as a sign of mourning. I did not care any more,” she says. “My husband died a long time ago and Latjor looked after me. I just don’t know what to do now.”

Although the food she receives from the airdrop will help feed her family for a little more than a fortnight, it is simply not enough, Kuony Tet says.

Walk around the market in Leer town and the need for airdrops – a costly and exceptional delivery method that the ICRC has not used since Afghanistan in 1998 – becomes apparent.

The remains of Leer hospital, which was attacked during clashes. Photograph: Nichole Sobecki/AFP/Getty Photograph: Nichole Sobecki/AFP/Getty Images

Among the charred ruins of the old market, which was destroyed in the fighting, people sell what little they have managed to grow or get their hands on: small piles of grain; packets of tea; local cigarettes and Panashiba batteries. The butcher, who hacks at pieces of goat on a bloody tree stump, has few customers, children scuttle over the scorched sheets of corrugated iron and a young woman begs for money to buy a single new sandal.

The conflict – which erupted after President Salva Kiir accused his vice-president, Riek Machar, of plotting a coup – has divided the country along ethnic lines, sparking bloodshed between Kiir’s Dinkas and Machar’s Nuers.

Tens of thousands have been killed; 1.1 million people – more than half of them children – have been displaced from their homes; almost 5 million are in dire need of humanitarian assistance; and predictions of famine in some areas look increasingly likely to be fulfilled.

Although the third and latest ceasefire appears to be holding in many areas, rivers remain unfished and crops unharvested. Unicef estimates that 50,000 children could die from malnutrition and warns of the loss of an entire generation of South Sudanese youth.

As the country prepares to mark the third anniversary of its independence from Sudan on Wednesday, the UN secretary-general, Ban Ki-moon’s, prophecy that half of South Sudan’s 12 million people could be either “displaced internally, refugees abroad, starving or dead by the year’s end” looks depressingly accurate.

To make matters worse, cholera has broken out, claiming more than 50 lives so far. Though the disease is under control in Juba, a fresh outbreak threatens those in the south-eastern county of Torit.

But even though the international humanitarian agencies are here in force, their white cargo and short-haul planes jamming the airstrip at Juba airport, and legions of their Land Cruisers on the capital’s streets, they face a crisis on an unprecedented scale. The UN says it needs at least another $1bn (£600m) to cope with the situation, and the Disasters Emergency Committee – which comprises the likes of Oxfam, Save the Children, the British Red Cross, and Cafod – says it has less than half the money it needs to deal with the situation.

Thousands of people wait for supplies near the drop zone in Leer. Photograph: Nichole Sobecki/AFP/Getty Photograph: NICHOLE SOBECKI/AFP/Getty Images

Ettie Higgins, the deputy representative in South Sudan for the UN children’s agency Unicef, counts off the challenges on her fingers. “You have conflict; you have no roads; you have a very intense rainy season where parts of the country are blocked off for six months of the year; you have no infrastructure; you have a very damaged private sector; and you also have banditry,” she says.

“You also have an underlying HIV/Aids crisis in parts of the country that shouldn’t be forgotten either because that disease spreads so easily in conflict situations. It’s this multiplicity of complications that makes it so difficult and so expensive to operate in South Sudan.”

Higgins, who has worked for Unicef in Zimbabwe, Darfur, Central African Republic (CAR), Somalia and Syria, says she has never seen a conflict “with all of these things rolled into one”.

But the problems do not end there: the ongoing strife in CAR, Syria and Iraq is makes competing for funds more and more difficult. Although Unicef is doing what it can to let donors know that the crisis will escalate if they do not pledge money now, Higgins knows it’s a tough sell.

“It’s not a big headline story,” she says, wearily. “The biggest news story from Africa at the moment is Oscar Pistorius. It’s not what’s happening in South Sudan, and I think that says a lot about what we’re struggling to deal with. We’re heading into the summer and I just think that people aren’t going to be interested in another bad news story.”

Sitting in his humid office at the ICRC compound in Juba, Franz Rauchenstein is similarly preoccupied with securing the funds to stop the crisis moving completely beyond control. But, like all the humanitarian staff in the country, the ICRC’s head delegate in South Sudan is wary of deploying the F-word.

“It’s difficult for us now to say we’re on the brink of a famine; additional things have to happen, but the signs are very, very clearly there,” he says. “There are high malnutrition rates in several areas of the country, and for the next year, these displaced people will need to be assisted with humanitarian aid.”

Families with malnourished children wait in Leer hospital for medical treatment. Photograph: Nichole Sobecki/AFP/Getty Photograph: Nichole Sobecki/AFP/Getty Images

Though the situation is dire, Rauchenstein says, the ceasefire has made a significant difference and there is still time to arrest the food crisis: “I would say the worst could be avoided if humanitarian workers can continue working and can reach those people who haven’t yet been reached.”

Things would be easier, he says, if clinics and hospitals across the country had not been looted and destroyed during the fighting.

The Médecins Sans Frontières (MSF) hospital in Leer is blackened and broken, proof of the repeated targeting of medical facilities. When the fighting reached the north of the country, the hospital was almost razed, its maternity unit and storage area gutted by fire and its supplies stolen or smashed.

When MSF’s expatriate workers were evacuated, local staff took all the medicine they could find and ran into the bush to set up clinics in the wilderness.

Sabrina Sharmin, an infectious diseases specialist from Bangladesh who worked at the hospital from 2009-10, hesitated when the charity asked her to return as project coordinator and supervise its restoration. She could not bear the idea of what had happened to her hospital. “I didn’t want to believe that it was true,” she says. “I hoped it was a myth.”

Today, slowly, the hospital is recovering: children are being treated for malnutrition, people are walking up to 40 miles to get treatment for HIV, tuberculosis and other diseases, and an incorrigibly effervescent German MSF worker uses a puppet called Mr Tom to teach visitors and patients about the importance of hand washing. But logistics are not what they once were. Records and treatment plans were lost in the fire, and the theft of all of MSF’s vehicles means that a donkey cart has to plod to the muddy landing strip and back every other day.

The gutted tuberculosis ward at Malakal teaching hospital. Medical and humanitarian staff were killed and facilities destroyed. Photograph: Matthew Abbort/AP Photograph: Matthew Abbort/AP

Although Sharmin is pleased she decided to come back, she struggles to understand what made people attack a hospital that had stood for 30 years and treated hundreds of thousands of people. As she walks there from her living quarters each day, she deliberately skirts the rusted and smashed container that once served as the storage room. She does not want to be reminded.

In Juba, too, people are subdued as independence day approaches and the peace negotiations continue to falter amid squabbling and recrimination. The South Sudanese flags that fluttered from cars on previous anniversaries are absent, the hawkers selling patriotic wares struggling for customers.

And at the drop site in Leer, where hope is in shorter supply than food, an unasked but inescapable question hangs in the air: how many of South Sudan’s people will live to see their fledgling country mark its fourth birthday?

Kuony Tet knows better than to hope for the best. “I am worried that they will come back and I am not convinced the peace will last,” she says. “Everything is unsettled.”