The whare will be located at historic points in the catchment and will tell the stories of the cultural and historical importance of each site.
A study of culturally significant species traditionally associated with the river will be undertaken and a cultural health monitoring programme developed.
Te Ropu Taiao o Ngati Whakatere kaiwhakarite, planting day co-ordinator, Robert Ketu, said their iwi had been working on the project alongside other affected hapu.
"The long and ongoing battles we have had with councils have brought us to a space where there is action taking place to restore the mana of the Manawatu River," he said.
Project executive Hone Morris said the overall purpose of the project is to enhance iwi involvement in the river's restoration, increasing its mana through communicating stories that reconnect iwi and hapu with their awa.
"Ko Manawatu te awa, he awa tapu, hei piringa mauri, hei piringa tangata. The sacred river of Manawatu, where the life force remains to bring people together," he said.
A culturally significant species protection and enhancement programme is planned for each of the whare sites, allowing iwi, hapu, whanau and students from local schools to engage in community science.
Tu Te Manawa project co-ordinator Arapera Paewai said it was a ground-breaking project.
"The National Cultural Health Index measures the mauri of an area by comparing the stories of the past to those of today," she said.
The $814,000 Tu Te Manawa project has received $534,000 from the Ministry for the Environment's Te Mana o Te Wai fund, $40,000 from Rangitane o Tamaki Nui a Rua, $220,000 from Horizons Regional Council, $10,000 from Palmerston North City Council and $10,000 from Tararua District Council.
The Manawatu River Leaders'Accord set the foundations for Tu Te Manawa by agreeing the state of the Manawatu River is unacceptable and that the community wanted it cleaned up.
Horizons natural resources and partnerships manager Dr Jon Roygard said council is committed to partnering with iwi, hapu and any other groups or people that share the same aspirations and goals.