The usual $2.75 fare has now been hiked to $4 a trip.
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Mayor Eric Adams said the base fare increase came as an effort to help fund the transit system.
But there are some discounts and deals available for riders.
A 10-ride ticket can be purchased for $27.50, allowing frequent riders to still pay the old rate.
There's also a new reduced $1.35 one-way fare for seniors, people with disabilities, and commuters who participate in the "Fair Fare" program, which offers half-priced MetroCards for those at or below the poverty line.
The NYC Ferry will send out two free ferry vouchers in the mail for new app users and to residents who live at NYCHA complexes within one mile of a ferry dock.
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The $1 bike fee was also eliminated across the entire NYC Ferry system to encourage sustainable alternative transportation methods.
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