Thousands of protesters jammed Copley Square on Sunday to protest President Trump’s order blocking Syrian refugees and immigrants from six other predominantly Muslim countries, the second time in the young Trump administration that Bostonians have flooded the streets in massive numbers to oppose the new president.

The protesters — people of all colors and faiths — filled the square from Trinity Church to the Boston Public Library, at the heart of one of the nation’s most reliably liberal strongholds, and steps from where bombers attacked the Boston Marathon nearly four years ago. They chanted: “No hate! No fear! Immigrants are welcome here!’’ They called Trump a racist and a fascist. They insisted he was violating the Constitution and vowed to resist him.

The demonstration, organized by the Massachusetts branch of the Council on ­American-Islamic Relations, began less than 12 hours after US District Court Judge Allison Burroughs and Magistrate Judge Judith Dein of Massachusetts imposed a seven-day restraining order against Trump’s executive order, permitting lawful immigrants from Iran, Iraq, Yemen, Somalia, Sudan, Libya, and Syria to enter the United States. The temporary ruling prohibits federal officials from detaining or deporting immigrants and refugees with valid visas or green cards or forcing them to undergo extra security screenings under Trump’s order.

Governor Charlie Baker, a Republican who did not attend the anti-Trump Boston Women’s March on Jan. 21, was once again a no-show. According to his administration, he was attending a funeral. His absence was noted by the crowd, which at one point chanted, “Where’s Governor Baker?’’

In a statement, Baker said his administration is trying to get a handle on how the executive order will affect the state’s residents, academic community, and medical and research sectors. A spokesman said Saturday that Baker opposes the executive order.

“The confusion for families is real,’’ Baker said. “The unexpected disruption for law abiding people is real. And the lack of guidance associated with such an abrupt and overwhelming decision is hugely problematic for all involved. . . . Thankfully, the federal courts will have an opportunity to straighten this out.’’

Despite the court ruling, it appears at least three passengers were detained for hours Sunday at Logan International Airport.

An Iranian woman who has been legally living in the United States arrived on an Emirates flight from Dubai that landed around 7:28 a.m., and was held for nearly three hours, according to her lawyer, Howard Silverman. Around 10:15 a.m., she was allowed to leave the airport with her husband, who is also from Iran.

Silverman, who declined to release his client’s name, said the early morning federal court ruling should have prevented officials from detaining his client. Still, he said, “We’re very happy she’s been released and she’s back with her family.’’

Later Sunday, Maryam Ghodrati received a text, sent from somewhere on the Logan tarmac. “We landed; let’s see how it goes,’’ Ghodrati said, reading aloud the message from her Iranian husband, ­Alireza, as she waited for him in Terminal E around 2 p.m. It didn’t go well; her husband would not emerge for another four hours.

Ghodrati, a PhD candidate at the University of Massachusetts Amherst, said she is a naturalized citizen; her husband, a PhD working in the area, has his green card. Their 10-year-old son was born here, and the family lives in Hopkinton.

She said her husband had returned to their home country of Iran on Thursday because his father had died. A day later, Trump issued his controversial executive order.

Worried about making it back into the United States, Ghodrati said her husband cut short his trip and missed his father’s memorial. He flew from Iran to Qatar for a connecting flight to Boston, where he was detained. He was ultimately released near 6 p.m. The couple embraced quickly and left without speaking to reporters.

In another instance, a PhD student in engineering management at Western New England University who declined to give her name said her friend Sona was detained after arriving at 1:45 p.m. from Dubai. Sona appeared a few hours later, hugged her friend, and spoke to an ACLU lawyer in Farsi.

State Representative Geoff Diehl, a Whitman Republican and former state cochairman of the Trump presidential campaign, said the Copley demonstration and others like it are “the next phase’’ of an effort by Trump opponents to obstruct the new president’s agenda.

“The former president, Obama, said elections have consequences,’’ Diehl told the Globe. “The fact is, a certain percentage of people in this country do want to have better security checks.’’ Trump, he said, is just keeping his promises. “I understand certain people may not agree on the policy, but it was something he made very clear on the campaign trail.’’

Mayor Martin J. Walsh, also a featured speaker at the Boston women’s march the previous weekend, told demonstrators Sunday that “discriminating against specific immigrant groups and religions is wrong.’’

City Councilor Tito Jackson, who has announced that he will challenge Walsh in the mayoral race this fall, told the crowd he stands “in unity with my Muslim brothers and sisters.’’

Massachusetts Attorney General Maura Healey was among 16 state attorneys general Sunday who blasted Trump’s executive order in a joint statement, pledging to use their offices to fight it. Joining Healey in the statement were attorneys general from New York, California, Pennsylvania, Washington, Hawaii, Virginia, Oregon, the District of Columbia, Connecticut, Vermont, Illinois, New Mexico, Iowa, Maine, and Maryland.

At the Copley protest, ­Fabienne Annylusse, 23, of Dorchester, said she worries about her Muslim friends.

“I believe what Trump is doing is deeply inhumane — immoral,’’ she said, noting her family had moved to Boston from Haiti. “We’re a melting pot. It’s just not right to ban anyone from this country because of their religion.’’

Laleh Golestani, an Iranian-Canadian biomedical engineer currently working at Harvard University, said she has colleagues who work locally in advanced medicine but as citizens of one of the banned countries can no longer attend conferences or see family members.

“I feel as if they’re going to come after me because I have Iranian blood — because that’s exactly what’s happening to many of my friends who are also dual citizens,’’ Golestani said. She moved to the United States three years ago. Golestani said Trump’s rise has her struggling to recognize the country she first knew.

“When me and my husband first moved here, everything seemed so stable,’’ Golestani said. “But when the news started breaking . . . I feel like a Jew during the dawn of Hitler.’’

Boston police said the protest was peaceful.

Astead Herndon, Jeremy C. Fox, David Abel, Nicole Dungca, and Maria Sacchetti of the Globe staff and Globe correspondents John Hilliard and Nicole Fleming contributed to this report. Mark Arsenault can be reached at mark.arsenault@globe.com. Follow him on Twitter @bostonglobemark.