The council said dredging the port basin area was essential to build and maintain the port, and improved dredging capability would also enhance the local boatbuilding and marine industry.
The plan for dredging the river came from community input on the project, specifically from the hapū collective Te Mata Pūau.
The collective is leading the project in partnership with the council and applying Tupua Te Kawa, the innate values of Te Awa Tupua.
It is also in place to ensure hapū members and the wider community are actively engaged in how the project is delivered.
The application is set to be filed this month.
If it is approved in 2022, dredging is anticipated to begin in the first few months of 2023.
The tender for the contract to build the wharves will go to market once all consents have been granted, with construction set to begin towards the end of 2022.
Two new entities have been established in order to access project funding the Government (through Kānoa - Regional Economic Development & Investment Unit) has agreed to contribute. This includes the creation of a council controlled organisation (CCO) called the Whanganui Port Limited Partnership, which is funded by the Harbour Endowment Fund and port operations.
The Whanganui Port Limited Partnership now owns and operates the port and its assets previously owned by the council.
"The council's work to revitalise the port, as part of Te Pūwaha, is firmly on track," council chief executive David Langford said.
"In a large scale infrastructure project like this, with several partners across several sectors, setting up a clear organisational structure is important in keeping matters related to funding and finances clear."
Te Pūwaha is a collaborative partnership between Whanganui hapū and iwi and the four other groups invested in the development - Whanganui District Council, Horizons Regional Council, Q-West Boat Builders and the Whanganui District Employment Training Trust.
The total investment in Te Pūwaha is more than $50 million, with the infrastructure works carried out over three phases. It includes $26.75m from the Government managed by Kānoa - Regional Economic Development & Investment Unit, with the remaining cost and resources covered by the two councils, Q-West and the trust.