Thousands of survivors of an Islamic State siege in the Philippines are stuck in makeshift dwellings more than two years after their city was liberated, with many forced to drink contaminated water despite the presence of EU-funded aid agencies.

They were among an estimated 350,000 people driven from their homes when Islamist fighters seized control of the city of Marawi, on the island of Mindanao, in May 2017.

Most assumed they would be back home within days, but the attack marked the start of a five-month siege, and more than 130,000 people remain displaced, according to the UN refugee agency, the UNHCR.

Driving through what remains of the heart of the city, it is not hard to see why. The worst-affected area remains in ruins. The walls of houses and mosques are pockmarked with bullet and shrapnel holes; pro-Isis graffiti is sprayed on walls alongside messages from property owners asserting their rights.

The ruined centre of Marawi, on the Philippine island of Mindanao. Photograph: Gethin Chamberlain/The Guardian

The soldiers at the entry checkpoint say most of the area is safe to enter, but unexploded bombs continue to be found in the wreckage and there is no sign of any rebuilding. The army reportedly wants to use part of the site as a military base and there has been discussion about creating a tourist resort, to the dismay of families who want to return to rebuild their homes and livelihoods.

Attempts to help those displaced have been further hampered by a breakdown in relations between the EU – a major aid donor – and the Philippine government.

In March 2017, the EU infuriated the Philippine government when it criticised the country’s war on drugs, which has claimed thousands of lives. President Rodrigo Duterte, who had responded to earlier EU criticism of his human rights record with a raised middle finger and the words: “Fuck you”, said the EU were “sons of bitches”.

For those hoping for help to go home to Marawi, the political spat was just one more disappointment among many.

Medine Dangcal stands outside the tiny shipping-container style home she now shares with her husband and six children at a camp for displaced people in Matungao, Lanao del Norte. It is hot in the daytime and cold at night, she says. They used to have a five-room house but fled when the shooting started.

Bonganga transitory site for displaced residents of Marawi, on the Philippine island of Mindanao. Photograph: Gethin Chamberlain/The Guardian

Nearby, sewing machines and microwaves are being unloaded from a lorry, part of a government “livelihood starter” project in partnership with the Catholic aid organisation Caritas. A sign in the centre of the camp proclaims it to be funded by EU civil protection and humanitarian aid. Various international NGOs are listed as helping with the response to the inhabitants’ “unmet humanitarian needs”.

Unfortunately, Dangcal explains, sanitation does not appear to be among the needs that have been identified. Her son has been sick for months, she says, and recently they found out that the water was contaminated.

Investigations have revealed the contamination is E coli, which can cause serious illness and death. Its presence is probably the result of animal faeces and human waste from overflowing septic tanks entering the drinking water pipes. A manager explains that problems began months ago, after the water supply was shut off following a local dispute and camp inhabitants began relying on rainwater and buying in jerrycans of water.

Mendine Dangcal with two of her children at the Bonganga site. Photograph: Gethin Chamberlain/The Guardian

In June, a UN assessment of camps, including the one at Matungao, reported worsening sanitation and an urgent need for more drinkable water. But nothing appears to have been done. An engineer at the camp says there are plans to replace some water pipes in a few weeks’ time.

Standing in the shadow of the camp’s empty water tower, Dangcal is unimpressed. “My child has been sick for three months. They promised to clean our water, but they tested it and it was contaminated,” she says. “I’m depressed and stressed. My business is gone. I have to get money from my relatives. We thought it would only be for two or three days, but we have been here almost two years. We want to go back to our town. I hate Isis. They made us give up our home.”

Other families don’t even have a solid roof over their heads. At the Sarimanok 2 transitory site, nearly 2,000 people are crammed into 175 tents. The dirty white canvas of many tents is cracked and ripped, with green mould at the base. The tents are set on dirt, with shallow drainage channels running outside.

Hassmin Domado’s tent leaks. The 27-year-old teacher has three children, including a baby. She says she wants to work again but can’t afford the 3,000 pesos (£45) needed to process the paperwork required, having left her home in Marawi. There is no aid programme to cover such expenditure. Her husband is managing to bring in 300 pesos a day (£4.50) working as a labourer. They have been there for two years.

Hassmin Domado, 27, at the Sarimanok 2 transitory site tents. A private teacher with three children, she escaped from Marawi and has been in the camp for two years. Photograph: Gethin Chamberlain/The Guardian

Like everyone else who was in Marawi on 23 May 2017, her mother, Hassana, remembers hearing the shooting start. Living on an island where various insurgencies have rumbled on since the late 1960s and gun ownership is widespread, Hassana, 46, says she wasn’t particularly concerned at first.

“We were thinking it was normal and it would be gone,” she says.

But when the mayor said they had five hours to get out, she left. She and her husband used to make a good living from a hardware store; now they have a small shop in the camp that brings in less than 1,000 pesos a day.

“We’ve been here for two years. They said it would be six months. I don’t think people are interested in us,” she says.

Down the road at the Boganga transitory site, Noraisah Usman Arumpac, 44, recalls leaving her children behind to lead her Christian friends to safety first.

“I knew my Christian friends were in a critical position as they wouldn’t be able to answer the questions from Isis, but my children would be able to answer them and they would be OK,” she says.

“The children were crying and asking why did we love our Christian friends more than our own children. But most of the Christians were being killed.”

She and her family have a roof over their heads and receive 5,000 pesos a month in cash aid, but they only think of returning to Marawi. “Why don’t they just allow us to go back and rebuild our lives? The government is always planning and planning.”

Bonganga transitory site. Photograph: Gethin Chamberlain/The Guardian

The EU remains optimistic that its aid programmes will be included in that planning – in the past two years it has donated €7m (£5.9m) to help people in Mindanao, including those affected by conflict – but while diplomats are clearly unhappy with the situation in Marawi, they are wary of pushing the Philippine government too hard.

“Once you’ve been burned you are afraid of the hot water – we don’t want to create a perception that we’re not willing to play ball,” says Enrico Strampelli, head of the development section at the EU delegation in Manila.

Diplomatic pitfalls are one of the few hazards that those living in the camps don’t have to negotiate. Cyclones and earthquakes are a constant threat, and children are particularly vulnerable to exploitation in the form of child marriage and child labour, with reports of girls as young as nine being offered as potential brides.

For Dangcal, like many others, the solution to the crisis seems simple: “President, can you let us go back to our land so our kids can live there and have a good life? I want my kids to see my native land where I lived.”