Water Taxi operates both a commuter service and a tourism operation.
The companies will continue to operate independently until the transaction is completed in December.
Tom Fox, who currently is chief executive officer of New York Water Taxi, will become CEO of the combined company. Further management appointments will be announced later.
J.B. Meyer, president and CEO of Circle Line Downtown, as the company is also known, said the two companies would join to form one of the largest tour and commuter ferry operators in the harbor.
"The businesses complement each other very well," he said.
Circle Line Downtown used to run ferry service to the Statue of Liberty, but another company took over that route this year.
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