Three Muslim mothers and their children were barred from boarding a city ferry due to a “security issue,” a complaint filed Thursday to the city’s Human Rights Commission claims.

The group of 11 family friends — including two moms wearing hijabs — were attempting to travel on the NYC ferry from the Wall Street pier to Brooklyn’s Pier 6, following an initial trip from Bay Ridge, according to the complaint.

But ferry personnel at Wall Street refused to let them aboard, citing a “security issue,” according to the document.

Pressed for further explanation, a worker shut the ferry gates and informed the women that “security” had told him not to let them aboard, the complaint says.

The women were then informed by security at the dock that they had been denied access because the children, who range in age from two months to 14 years, had been standing on seats.

The families, according to the complaint, “believe this was an after-the-fact false excuse in an attempt to explain away… discriminatory conduct and denial of services.”

They wound up waiting two hours to board — ultimately deciding to nix the trip to Pier 6 after the children became distraught and started crying.

“[Their] entire day was ruined,” the complaint said. “[The families] were embarrassed and humiliated, especially since the incidents… occurred in public view of all ferry passengers.”

As part of the complaint, the families are seeking a “formal apology,” unspecified damages and for the two employees involved to be disciplined.

Ferry ridership data shows that riders are largely white and wealthy.

Hornblower, which operates the ferries on behalf of the city’s Economic Development Corporation, did not return a request for comment.

“Discrimination has no place in our city,” an EDC spokesperson said in a statement. “The city is investigating these allegations, and if they are proven true, will take swift and appropriate action to hold those responsible accountable.”