An agreement between the Crown and local iwi on what the values will be in protecting the river are yet to be decided.
A whole river strategy, in collaboration with iwi, local government and commercial and recreational users is still being decided.
An eventual settlement will also include monetary compensation for historical claims.
Minister for Treaty for Waitangi Negotiations Christopher Finlayson said the signing was an historic event.
"Whanganui River iwi have sought to protect the river and have their interests acknowledged by the Crown through the legal system since 1873. They pursued this objective in one of New Zealand's longest running court cases.
"Today's agreement which recognises the status of the river as Te Awa Tupua (an integrated, living whole) and the inextricable relationship of iwi with the river is a major step towards the resolution of the historical grievances of Whanganui iwi and is important nationally.
"The agreement does not signify the end of the settlement, but it is a significant step towards settlement. Matters of detail and additional redress will be to be negotiated between the parties," said Mr Finlayson.
"Whanganui Iwi also recognise the value others place on the river and wanted to ensure that all stakeholders and the river community as a whole are actively engaged in developing the long-term future of the river and ensuring its wellbeing," said Mr Finlayson.
History of the claims:
* Those parts of the Wai 167 claim relating to the Whanganui River were heard by the Waitangi Tribunal in 1994.
* The Tribunal issued its Whanganui River Report in 1999.
* The Crown vested authority and control of the Whanganui River in local authorities through the Resource Management Act in 1991.
* Negotiations between Whanganui iwi and the Crown in relation to the Whanganui River took place between 2002 and 2004.
* Discussions between Whanganui iwi and the Crown started again in 2009.
* A record of Understanding reached on October 13, 2011 outlined a framework for the next stage of formal negotiations.
* The final settlement including the deed of settlement in relation to the historical Treaty of Waitangi claims of Whanganui iwi in respect of the Whanganui River are yet to be decided.