Work to demolish the terminal building and upgrade St Helier's Albert Pier is due to get underway over the next few months.
If the £5 million plans are approved, new pontoons will be created accessible by boat owners 24 hours a day.
Ports of Jersey says they will also allow some of the harbour's larger boats to be moved, creating 20 new berthing spaces elsewhere in the marinas.
The Albert Pier Terminal is also set to be demolished. It has been empty since Manchés Illes Express relocated to the nearby Elizabeth Terminal.
Albert Pier Terminal in 2008, when it was more frequently used.
Local contractor Geomarine has been chosen to carry out the work, which will be solely funded by Ports of Jersey without any government support.
Steve Tanner, Ports of Jersey's Capital Projects Manager says the project has been planned for some time and originally due to be carried out in 2020, but had been delayed:
"We’d hoped to start work on this project last winter, but our proposals were put on hold for 12 months while we focused our efforts in dealing with the coronavirus pandemic.
"We have consulted and engaged extensively with our commercial operators and leisure users who have welcomed the plans and recognise the opportunities and benefits this reconfiguration of the Albert Pier will bring to leisure marine community".
The work was planned for the winter months, which Ports of Jersey says was to minimise disruption to harbour users.
CEO for Ports of Jersey, Matt Thomas, says it's an important investment in the island's marine infrastructure:
"Despite the impact of Covid-19 and the challenging times we face, the need for investment in St Helier Harbour has not changed.
"Ports of Jersey is committed to investing in our harbour infrastructure to support the resilience of the Island’s lifeline services and supply chain, as well as the future sustainability of our maritime industries.
"We look forward to sharing our broader investment plans for the development of the harbour when the current demands of the pandemic have passed."