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Four years ago, Mayor Bill de Blasio unveiled a plan to spend more than $325 million on a fleet of custom-built ferryboats and docks so that more of the city’s neighborhoods would have a better transit connection.

But since then, the costs of starting up a ferry service that links all five boroughs have almost doubled from Mr. de Blasio’s original commitment, which has drawn criticism from transit advocates, elected officials and government watchdogs. One complaint is that the service caters mainly to higher-earning residents at a time when the subways are still in need of repair and state officials are preparing to charge drivers to enter Manhattan’s busiest areas.

The mayor has called such criticism “very shortsighted.” He has argued that the ferry service is providing a fast, affordable commuting option to neighborhoods that had long been “transit deserts.”

On Wednesday it’s expected that city officials will have an opportunity to defend the mayor’s plan during a City Council hearing, where a committee will consider giving the city more say over how and where the ferries operate.