The WCO has proved controversial within the community.
The application was made by six groups in 2015, New Zealand Fish and Game Council; Hawkes Bay Fish and Game Council; Operation Pātiki Ngāti Hori ki Kohupātiki; Royal Forest & Bird Society of New Zealand; Whitewater NZ and Jet Boating New Zealand.
It has been opposed by primary industry groups including Federated Farmers and Horticulture NZ, as well as by Hawke's Bay Regional Council, which was concerned about the impact a WCO would have on its TANK plan change process.
Spokesperson for the co-applicants, Tom Kay, said the decision did not go as far as they had hoped, however it was still a win for the health of the river.
"New Zealand has very few rivers like the Ngaruroro," Kay, from Forest and Bird, said.
"The upper reaches of the Ngaruroro are about as close as you can get to pristine.
"It's an amazing landscape, the water is crystal-clear, there's incredible whitewater kayaking, and a renowned trout fishery."
He said they were disappointed a WCO was not put in place for the lower part of the river, and were considering whether to take further action during the 15-day submission period applicants have to air concerns.
CEO of Hawke's Bay Regional Council, James Palmer, said they are pleased the recommendation is not to have a WCO on the lower section of the river.
"In light of the clear factual findings by the Special Tribunal, the Regional Council looks forward to progressing both current and future planning processes to appropriately manage and guide resource management in Hawke's Bay.
"The Council looks forward to working with the applicants in these planning processes."
The Conservation officer at the Hawke's Bay Canoe Club, Bernie Kelly, said from a kayaking perspective the recommendation was a win.
The recommendation protects the area of the river which is significant for whitewater kayaking, which Kelly said was used by kayakers from across New Zealand.
"It's a big win for us," he said.
Federated Farmers Hawke's Bay president Jim Galloway said he was pleased the recommendation was not to have a WCO on the lower half of the river.
"We were concerned that it would impinge on our ability to take water for stock drinking and domestic supply.
"And the proposed water quality limits could have prevented the maintenance of a farm's normal seasonal variation; our livestock numbers differ hugely from summer to winter depending on pasture growth."