It was a Memorial Day weekend to forget for riders of the city’s beleaguered $600 million ferry service on Sunday — as they faced massive lines, skipped stops and overcrowded boats along the Big Apple shore.

Lines for the Rockaway Beach route at Wall Street’s Pier 11 stretched for several blocks by midday, forcing angry travelers clad in swimsuits and cradling beach chairs to endure waits up to 90 minutes in the boiling sun.

“I am very angry that they don’t have a better system, more shading, giving water to the passengers — I’m very upset,” said NYU student Colle Serrano, 25, who had been waiting in 80-degree temperatures while nursing a pair of recently broken ribs.

“I am overheated!”

Riders at the Sunset Park dock in Brooklyn faced the ultimate frustration when the Rockaway-bound ferries — already packed with passengers from the Wall Street stop — were unable to pick them up on their way out to the beach.

The holiday weekend boondoggle was just the latest black eye for NYC Ferry.

Mayor Bill de Blasio’s Economic Development Corporation (EDC) has sunk at least $582 million into the service — one of his signature transportation initiatives — since it was launched in 2017, according to a tally from city Comptroller Scott Stringer.

But the system carries just 13,000 people per day on average, with a recent study showing it has an operating subsidy of $10.73 per ride — double what it costs to run the Staten Island Ferry.

Earlier this month, City Hall rammed through its controversial plan to spend $84.5 million to buy 19 boats already operating as part of NYC Ferry, despite repeated objections from the comptroller’s office due to the service’s ballooning costs.

Beachgoers excited by Sunday’s above-average high of 83 degrees wondered why officials didn’t put more boats into operation for the holiday weekend rather than keep the normal Sunday schedule.

“I am not happy,” said Russell Bookert, 38, a Brooklyn teacher who had been waiting more than an hour for a Rockaway-bound ferry at Pier 11. “We are frustrated because they do this every single year. It’s wrong.”

“They said they were going to get more ferries, but they never do.”

The EDC said it chartered four extra vessels and put 20 agents at the busiest stops, but it did little to stop the meltdown.

“We’re running the maximum amount of service possible to clear wait times and ask riders to check the app for real-time updates,” an EDC spokeswoman said.

Serrano groused about the fact that passengers were not warned of delays.

“The applications don’t tell you there is a delay. They don’t tell you that there is going to be a passenger limit. That makes me even angrier because I’m not getting any information.”

The delays hit other routes, too. Some boats out of Soundview in the Bronx were so full, they could not pick up passengers at the second stop on East 90th Street near Gracie Mansion.

Stranded passengers there included City Councilman Ben Kallos, who blasted NYC Ferry on Twitter.

“The ferry should NOT leave people behind on the first stop,” he wrote.

Laura Picallo, 36, from Astoria, Queens, said she had thought the ferry would be quicker than the A train, but told The Post, “I will not do this again,” calling the wait “outrageous.”

“I have been waiting in line for an hour and a half, and I am angry,” she said.

“I expected to walk onto a boat and to have a small wait. But nothing like this. This is crazy. There should be more boats because it’s Memorial Day weekend.

“I’m taking the train the next time.”

It was pandemonium on the way home, too, with lines becoming nightmarish around 5 p.m. as thunderstorms washed away beach plans and hundreds of New Yorkers swarmed the Rockaway Beach landing.

Other riders also swore off taking a ferry on future Memorial Day weekends.

“We’re on this line for 45 minutes. It’s awful,” said Kristen Ryan, 54, who watched two Big Apple-bound boats pass before she eventually got on the third one with friends.

Yet NYC Ferry has no plans to increase service on Memorial Day, warning riders of even more delays and disruption Monday.

“We won’t do it again,” Ryan said. “It was basically an hour waiting each way, waiting for the third ferry each way, so no, I wouldn’t do it again. Ever.”

Additional reporting by Allie Griffin