The Harbour City Ferries consortium, made up of Transfield Services and Veolia Transdev, has begun the $800 million, seven-year contract to maintain and operate the ferry services.
NSW Transport Minister Gladys Berejiklian said handing over the operations of the ferries had been a smooth transition.
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"Customers won't notice the difference in the next few weeks," Ms Berejiklian told reporters in Sydney.
"But we're confident that they will notice the difference in the months ahead when customer service is enhanced and we provide additional parts of our great waterway."
The NSW government has already restored 140 ferry services scrapped by the previous government and provided an additional 25 weekly services along the Parramatta River, Ms Berejiklian said.
Fifty of Sydney Ferries' 600 employees transferred to the new organisation, with the remaining staff accepting voluntary redundancy or support for redeployment.
The employees that have left will be replaced.
