They have caused billions of dollars of damage to the economy and more than 1,300 deaths.
The grim situation in Khyber Pakhtunkhwa has left the camp's inhabitants at the mercy of the elements, living under open sky without government support as winter closes in. Night-time temperatures in northern Pakistan drop sharply in November.
Nargis Bibi, a 60-year-old mother of 10, was shocked to learn of the flooding when someone from the neighbourhood knocked on her door at night, telling her that waters in the Kheshgi village camp were rising.
Many of the buildings in the camp are basic but semi-permanent dwellings that stood little chance against torrents of water.
The camp is in Nowshera city in Khyber Pakhtunkhwa province, on the bank of the river Kabul, which overflowed and inundated the town.
Traumatised by the flood alert, Ms Bibi called for local youths to rescue her paralysed husband and children from the flood.
“For God’s sake help me save my husband and children, forget about the goods and items,” she recalled telling locals that night, her voice shaking.
Her husband and children were evacuated to a safe place nearby, from which she saw her house destroyed in an instant in a torrent of water.
Pakistan’s recent flooding was caused by torrential rains and has wreaked havoc across the country, injuring more than 12,000 people — in addition to the 1,300 killed — and affecting 33 million, according to the country’s National Disaster Management Authority.
More than 1.7 million houses have been partially or fully damaged by the flood, the NDMA said.
“I have nothing in hand except for the temporary shelter that is now swept away by the flood, I have nowhere to go now, Ms Bibi said, looking at her children and ailing husband.
Her plight is identical to that of the 2,000 registered Afghan refugees who live in temporary shelters in Kheshgi village camp.
A legacy of war
About 1.3 million Afghans live in Pakistan, refugees from decades of conflict.
In an attempt to compensate those affected by the floods, the government has distributed relief packages to hard-hit communities, but the Afghan refugees are not eligible for compensation.
Some of them have migrated several times, fleeing invasions and civil wars in their home country.
Mirza Ahmad, 65, who lost everything in the flood, has been displaced twice before.
In the early 1990s, he was forced to leave Jalalabad province in Afghanistan, when the country was slipping into civil war, following the end of Soviet occupation and the collapse of the Russian-backed government.
He first migrated to Akora Khattak refugee camp in Nowshera district of Khyber Pakhtunkhwa.
However, that camp was hit by flooding in 2010 and he was displaced again.
Digging through shattered wood, debris and mud in the scorching heat, he struggled to recover his possessions while people sat in the shade of nearby trees.
“I have nothing left as everything has been swept away by the flood. Only the memories flash in my mind,” he said.
The only breadwinner for his 11 member family, Mr Ahmed says he lost two shelters in the flood.
“I have to find another place to live, because the owner of this land will not let us build this home again. I’m old and weak now. It would be difficult for me and my family to spend the rest of our lives under the open sky.
“We are waiting for a miracle to happen. We were in serious need of water and food. No government institution has come to our help.”
Mr Ahmad has received support only from non-profit organisations. He lamented that the government had yet to ask about their plight.
“The locals have supported and helped us, but that too was not sufficient,” he said.
Hearing of the plight of the refugees, social media activists highlighted the issue, finally leading to support from the UN High Commission for Refugees and local welfare organisations, which have provided tents, food and water.
Another woman from the refugee camp, 55 year-old Bushra Bibi, said her daughter-in-law was seven months pregnant.
“After the flood, my daughter-in-law hasn’t eaten anything for several hours because there was nothing to curb the hunger,” she added.
She begged for any food available, Ms Bibi recalled, even bread soaked in water.
“We were looking to the sky, crying for food like birds waiting for their mother to bring food to its beak,” Ms Bibi said.
The UN Population Fund says nearly 650,000 women are stranded in flood affected areas, requiring immediate maternal health services to ensure a safe pregnancy and childbirth.
Taimur Ali of the provincial disaster management authority in Khyber Pakhtunkhwa confirmed that the government had not announced any special grants or help for the refugees.
By contrast, he said the UNHCR had reached the refugees, distributing tents, food, cooking stoves, blankets, solar lamps, sanitary products and sleeping mats.
However, the refugees say the items provided are still not sufficient to meet their food and shelter needs.