Many undocumented Afghan migrants have Pakistani spouses and have lived in the country for years. Nevertheless, the government says they must leave.

Every night in Karachi, a bustling port city in Pakistan, Fatima Bibi goes to bed in fear. The sound of police sirens from the streets outside makes her anxious. She wonders whether a knock at the door might tear her family apart.

Her husband, Sher Zada, is an Afghan refugee. His family fled conflict in Afghanistan when he was just a boy, in 1992, and Pakistan is the only home he knows. Ms. Bibi’s family long hoped that despite Mr. Zada’s undocumented status, his close ties to the country and marriage to a Pakistani national would eventually help him secure permanent residency, if not citizenship.

But to the Pakistani government, it is officially past time for Mr. Zada to leave.

On March 31, a government-imposed deadline expired for many Afghans in Pakistan to find another country of refuge. Those without legal status who remain in Pakistan, like Mr. Zada, now face repatriation. Less than three weeks after the deadline’s expiration, the Pakistani minister of state for interior, Talal Chaudhry, announced at a news conference that more than 80,000 Afghans had already been expelled.

The deportations could subject the refugees to perilous conditions under the heavy hand of Taliban rule in Afghanistan. And, if they are married to Pakistanis, it could mean leaving their families behind.

The campaign to deport Afghans coincides with a resurgent conflict with India, Pakistan’s eastern neighbor and archrival. India has ordered almost all Pakistani citizens to leave the country, part of its response to a terrorist attack in Kashmir that it has linked to Pakistan. The Pakistani government, which denies any involvement in the attack and has asked for an international investigation into it, responded by canceling most Indian citizens’ visas.

Pakistan’s crackdown on Afghans follows years of tightening restrictions on Afghan residency. Recent U.N. reports indicate that over 910,000 Afghans have been deported from the country since September 2023.

The deportations have been motivated largely by officials’ frustration with the Taliban government, which they accuse of harboring Pakistani militants responsible for deadly attacks inside Pakistan. The Taliban deny those allegations, but tensions continue to rise.

Pakistan’s military said on Sunday that it had killed 54 militants trying to infiltrate the country from Afghanistan over the previous two nights. Pakistan said the militants had been “khawarij” — a term it often uses for the Pakistani Taliban.

The Pakistani government has also been emboldened by a tide of anti-immigrant sentiment around the world. It has drawn parallels to recent deportation efforts in the United States and various European countries to justify its own campaign.

Among the Afghans facing deportation in Pakistan are those who arrived after the Taliban seized power in August 2021 and now await resettlement in Western countries, including the United States. Pakistan extended the deadline for their relocation to another country to Wednesday, after which they will again face deportation.

Their fate became increasingly uncertain in January when President Trump issued an executive order suspending all refugee admissions to the United States. The decision left thousands of Afghans stranded in Pakistan with no clear recourse.

In October 2023, during an earlier wide-ranging effort to expel undocumented Afghans, Mr. Zada was detained. He narrowly avoided deportation only after Ms. Bibi’s father paid a last-minute bribe to secure his release.

This year’s renewed deportation campaign forced Mr. Zada and his family to leave their home. Ms. Bibi’s father offered them shelter, putting himself at risk. At the news conference this month, Mr. Chaudhry warned of strict repercussions for anyone who helped Afghans stay in the country illegally.

Rights groups say that the plight of refugees like Mr. Zada — Afghans married to Pakistani citizens — is one of the most overlooked aspects of Pakistan’s deportation drive.

While no official data on the subject is available, rights groups like the Joint Action Committee for Refugees, a Pakistani civil society network, estimate that thousands of Afghan-Pakistani marriages have taken place. They are especially common in parts of Khyber Pakhtunkhwa and Balochistan, Pakistani provinces that share a porous border with Afghanistan.

Such weddings are often conducted through tribal customs or informal community ceremonies. Though socially recognized, the unions frequently lack formal documentation, such as marriage certificates, making it hard for the Afghan spouse to obtain legal residency or citizenship.

Even in big cities like Karachi, Afghans with Pakistani spouses often face obstacles to formally registering their marriages or the births of their children.

Legal experts have told Mr. Zada that his marriage to Ms. Bibi gives him a chance, if a slim one, of staying in Pakistan legally. But the lengthy process and the high fees are prohibitive. Mr. Zada earns just $3 a day, he said.

Some Pakistanis married to Afghans have turned to the judiciary for relief from the bureaucratic obstacles. In July, a court in Khyber Pakhtunkhwa ruled in favor of 65 petitioners, affirming that their Afghan spouses were eligible for dual nationality. But such cases are uncommon.

Umer Ijaz Gilani, an expert on refugee rights based in Pakistan’s capital, Islamabad, said the authorities had deliberately fostered the perception that refugees had few options for obtaining legal residency or citizenship, despite constitutional guarantees and numerous rulings from higher courts.

Refugee-rights activists also say that NADRA withholds origin cards from applicants who qualify, often citing the need for clearance from Pakistan’s intelligence agencies. NADRA officials declined to comment on those claims.

The Pakistani authorities remain firmly committed to the deportation campaign. Officials say that all undocumented Afghans must leave the country and re-enter on valid visas, regardless of marital or familial connections. But current immigration restrictions can make it almost impossible for them to secure visas after they leave.

Mukaram Shah, an undocumented Afghan migrant married to a Pakistani woman, had been living on the outskirts of Quetta, a city about 70 miles from the Afghan border. In December 2023, he was arrested by the police while working as a porter at a local vegetable market.

“We could not even say a proper goodbye,” said his wife, Palwasha, who, like many women from rural Pakistan, goes by a single name.

Her family, citing security and economic concerns, refused to let her follow her husband, believing he would return on a long-term visa. But under the current crackdown on Afghan refugees, that hope is fading.

“Every night, my children ask when their father will come home,” Palwasha said, her voice breaking. “I don’t have an answer. All I can do is pray.”