Memorial Day weekend brought fresh dysfunction in Mayor Bill de Blasio’s ferry system, as hundreds of riders roasted in the sun as they endured long waits and even watched boats skip their stops.

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Lines for the Rockaway Beach route at Wall Street’s Pier 11 stretched for blocks Sunday, with waits above 90 minutes for furious New Yorkers clad in swimsuits and carrying beach chairs.

Would-be vacationers at the next stop, the Sunset Park dock in Brooklyn, had it worse — as Rockaway-bound ferries, already full, motored right on by. And boats that filled up at Soundview in The Bronx couldn’t take passengers at their next stop on the East Side.

These snafus highlight an essential flaw in the thinking behind the $600 million NYC Ferry program: De Blasio imagines it’s for commuters, but lots of people see it as more recreational. Hey, there’s a bar!

Even with the fare held to $2.75, that latter class of consumer is unlikely to help the system grow beyond its current 13,000 passengers a day — too small-scale to be remotely cost-effective. (Nor does it make sense to subsidize holiday boats.)

As things stand, the Citizens Budget Commission reported recently, the city is kicking in an average of $10.73 for every ferry rider, on top of the fare. All to add practically nothing to the transit system.

That’s 10 times the per-ride subsidy for New York City Transit subways and buses, which move millions each day.

Spending on the ferry is one of the issues where City Council Speaker Corey Johnson is demanding more transparency in the council’s budget fight with the mayor.

Stand firm, CoJo.