The city’s new ferry service counted its one millionth rider Wednesday — just three months ­after launching in May.

The milestone outpaced projections by a month, Mayor de Blasio said. He also reminded New Yorkers that on on Aug. 29 the city will launch a fourth ferry route, connecting Astoria, Long Island City and Roosevelt Island with Manhattan.

“We know there’s been some challenges,” he said at a press conference in Queens. “The blessing is a lot of people like it. The challenge is a lot of people have shown up — more than expected.”

So far, the East River route is the most popular, with more than 625,000 riders. The Rockaway route has counted 221,000 and South Brook­lyn 154,000.