As Europe grapples with the biggest wave of migration since World War II, the fates of those crossing the Mediterranean are increasingly being determined by class systems based on money, ethnicity and religion.

On these transnational trails, migrants tell of a fast-developing market for human cargo, where cash or creed can ensure a safer trip, more resources and better treatment.

The discrimination starts at the beginning of migrants’ journeys at the hands of smugglers looking to maximize profits, and it ends with European authorities scrambling to handle the overwhelming numbers of people arriving and prioritizing them by nationality.

In Greece this weekend, authorities deployed a 3,000-capacity passenger ferry to the island of Kos to host Syrian refugees arriving in record numbers. Thousands of other asylum seekers on the island from Iraq and Afghanistan have been left without shelter, and with only sporadic access to food and a much longer wait to get their documents processed.

Syrians are prioritized because the United Nations High Commissioner for Refugees has advised governments that they are so-called prima facie refugees, meaning they should be granted instant humanitarian protection because they are fleeing a war zone.

European Union countries recently agreed to resettle some 32,000 refugees from Greece and Italy, but said they would only do that for Syrian and Eritrean nationals, both designated as prima facie refugees by the U.N.

First reception procedures should be the same for everyone, said Barbara Molinario, a spokeswoman for the U.N. agency. Syrians are considered prima facie refugees, but “people from other countries might also have valid refugee claims, and generalizations should be avoided,” she said.

On Kos, many locals view Syrians—who are almost neighbors across the Aegean Sea—as culturally similar to them. “Syrians are more civilized and they show more respect,” said Lefteris Kefalianos, a Kos resident who sells construction materials.

Some 124,000 refugees and migrants arrived in Greece by sea between January and July this year—a 750% increase from the same period last year, according to the U.N. On Kos, an island of some 33,000 residents, more than 22,000 have landed since January and local authorities estimate about 4,000 are currently on the island.

Elsewhere in the Mediterranean, boats ferrying migrants to Europe from Turkey and Libya are offering a two-tier pricing system, allowing safer seats on deck for those with financial means. On Saturday, 40 migrants locked in the hull of a wooden boat died in a pool of “water, fuel and human excrement” according to the Italian navy; those sitting on the upper deck survived.

Once in Europe, some more affluent migrants can afford to book hotel rooms while their papers are processed. “Among the migrants, I have been getting mostly Syrian people,” says Yannis Sotiriou, owner of Camelia hotel near Kos’s busy port. Other hotel owners said they turn away other migrants because Syrians are seen as more respectful.

Arezo Malakooti, a senior researcher with Altai Consulting, a firm that conducts on-the-ground investigations for the U.N. refugee agency, said the historic migration wave reaching Europe was becoming “intensely commercialized,” with migrants being treated increasingly like “market commodities,” with a clear hierarchy based on means and nationality.

“Smugglers really are motivated by money, but anecdotal evidence also suggests Muslims are treated better in Libya” she said.

The testimony of migrants traveling the booming routes from Africa and the Middle East show how nationality and faith can sometimes be a passport to safety; at others, abuse and extortion.

The starkly differing conditions of migrants pouring into Europe are causing mounting friction. Over the weekend, fights broke out among different nationalities of asylum seekers on Kos over the little attention they were getting from authorities and the seemingly better treatment of Syrians.

“Syrians are refugees, the others are immigrants,” said Zacharoula Tsirigoti, head of the border-protection branch at the Greek police Friday, when asked why the Kos ferry would host only Syrians.

In other parts of Europe, governments are arguing that Christians should get assistance because they share similar values to the local population. Most recently, the Slovak government said it would only help resettle Christian refugees.

Del Haca, a 22-year-old Afghan man on Kos with his pregnant wife, says that neither had eaten in two days. They have been on the island for nearly a month, waiting to be processed.

The long crossing of the Mediterranean from North Africa to Italy remains among the world’s deadliest migrant journeys. The U.N. says more than 2,500 have died attempting it since the start of the year.

In Libya, the hub for the lucrative trade in migrant smuggling from Africa to Italy, the system determining migrants’ survival is based primarily around wealth, migrants said.

Smugglers there aim to maximize profits through a web of extortion, abuse and ultimately price differentiation.

“Syrians have put more money together, they are able to pay more so they’re placed at the top level of the boat and sometimes even buy life jackets,” said Ms. Malakooti of Altai Consulting.

“Sub-Saharans are put in the hulls. If the boat takes water, they’re the first to drown,” she added.

Lamin Wandi Dampha, a 17-year old Gambian, was in the belly of a boat for two days in April.

“There was no food, no water, no light, no toilet,” he said, at a reception center in Pozzallo, Sicily. He said he paid the smuggler $300, whereas many Syrians say they pay as much as $1,800.

His story was corroborated by more than a dozen other young men from Senegal, Gambia and Nigeria at the same Italian reception camp.

African Christian migrants said Libyan smugglers abused them out of racism or hatred for Christianity. The claims couldn’t be independently verified. Amnesty International detailed abuses targeting African migrants and refugees in a May report that said minorities—unaccompanied children, women and Christians—were singled out for torture at the Libyan smuggling camps where thousands languish before being boarded on the boats to Italy.

“They called me hamar [Arabic for “donkey”] and beat me every day for four months,” said Mike Ikechikum, a 27-year-old Nigerian at Pozzallo camp.

Mr. Ikechikum found himself in a tragically common situation: having paid about $500 to get to Libya from his village in northeastern Nigeria, he didn’t have the $300 the smuggler was asking to get him on the boat to Italy.

To save for the trip, he was forced to work for no pay for four months as a car mechanic near Tripoli to earn his boat fare.

Often, such abuses stop when cash changes hands, experts and migrants say.

Smugglers in Libya for example tend to believe Eritrean refugees, who are often Christian, are worth more money than West Africans, because many have wealthier families in Europe, according to researchers and Eritrean refugees. They abuse or kidnap Eritreans and extort their families, getting payments of thousands of dollars from relatives abroad.

Mr. Dampha, the Gambian teenager, didn’t have the money to stop his smugglers when they turned into abusers in Libya.

“They wanted 500 dinars ($365) to stop beating me with hot metal, but I didn’t have it,” he said, pulling down his trousers to reveal a wound spreading from his left hip to his knee. “The people here gave me medicine. By the grace of God I am here alive.”