The ferry that brings Rockaway and south Brooklyn to Manhattan will continue riding the waves, but at a higher fare for passengers.

Mayor Bill de Blasio Tuesday said the Rockaway ferry service will cost $3.50 a ride, from $2 previously, and operate until May, with an option to extend it until August. The city's Economic Development Corp. will also solicit proposals from ferry operators to keep the Rockaway service in operation permanently.

"We're developing the Request-for-Proposal process to see which providers might be able to continue the service going forward on a cost-efficient basis," de Blasio said.

EDC spokeswoman Kate Blumm said the fare hike for the Rockaway ferry will help offset the cost of the city's high subsidy for the service. She said a city subsidy will be necessary to keep it afloat in the future.

"The ferry has proved to be tremendously valuable to Brooklyn and Queens residents, and we look forward to exploring the potential for sustainable long-term operation along this route," Blumm said.

The ferry has been at risk of discontinuation since the service was instituted in November 2012 as a temporary way for Rockaway residents to get to Manhattan after Superstorm Sandy knocked the A train out of operation. The Rockaway ferry has since added a stop at Brooklyn Army Terminal to serve Bay Ridge and Sunset Park residents who have been without a connection to Manhattan on the R train since the MTA started repairing the Montague tunnel in August.