At the heart of the debate is that the WCO could take away the power of the Hawke's Bay community and local leaders to make decisions about the use of water from the two rivers - which could impact the local economy.
Many feel the local planning process TANK is a better approach - this community-run water management project aims to set limits, measures and a monitoring regime to manage water in the Tutaekuri, Ahuriri, Ngaruroro and Karamu/Clive catchments.
Its job is to protect water resources - in the way the WCO seeks to do - while balancing this with the needs of the local community, and economy.
TANK is led by the Hawke's Bay Regional Council. Its chairman Rex Graham is among those angry that some of the applicants had been involved in the early stages of TANK, and had entered into the WCO process knowing it would affect TANK.
"Every time I think about what happened I get madder and madder because it is a breach of our community right to be able to discuss things, and come to their own resolutions."
In comparison to the WCO, TANK was the product of different stakeholders across the region doing what they thought would be a good outcome for the TANK catchment, Federated Farmers Hawke's Bay president Will Foley said.
"I think the TANK catchment is in a really good space already. There's a lot more information we can collect and research but thus far it seems to be in a good state.
"I don't see why we can't keep it in a good state or improve it while keep going with a profitable and productive sector in that catchment."
In trying to ensure balance between the environment, and the economy, he said he thought there would have been more buy-in from locals for a regional process - rather than a national one.
"That's why TANK looked like it was going to be so successful because it was totally local people being part of that process.
"We can have a really good environment, and we can have a really good economy at the same time, we just have to be smarter about how we do it," he said. "As time goes on we learn more, research more, and know how to do things better."
The impact of the WCO on the local economy has been a catch-cry of the high-profile campaign against it.
One of the key figures, Twyford Irrigators Group spokesman Jerf Van Beek, has said the WCO would have a "devastating impact", arguing it would be detrimental to the local economy, and could result in job losses.
Some opponents have put forward figures suggesting as many as 2000 jobs could be lost if the WCO goes ahead, as outlined in the application.
For Mr van Beek, flexibility is his key concern: "The WCO is a piece of legislation that we can't really live with, because once it's in place it's forever and a day in place.
"I think if we're going to entertain legislation that is not changeable in future then we're not actually doing the best thing for the community, or the environment because we don't know what the environment is going to look like in future."
He said the WCO could result in small changes, that would have "major effects" in how those in the primary sector operate, and that users might not be able to adapt their water use for changing seasons, or their needs.
Those among the horticulture and agriculture sector have shared concern that under the WCO consented water take volume could drop dramatically, and see an increase in minimum flows which would increase the number of irrigation ban days.
Although the applicants have stated the WCO would not alter existing consents, some worry it could affect consents when they come up for review, and renewal.
Consents are issued by the regional council. Mr Graham said presumably the existing consents would have to operate to the water levels in the river that the WCO sets, "therefore most of them will be useless".
"Of course there'll be existing consents but they'll be bloody useless because you'll be on ban half the time," he said.
"[The applicants] are in total denial on the effects it's going to have on the community."
There is currently a moratorium of sorts on new consents for water takes from the Heretaunga aquifer, based on science from TANK.
When asked how TANK would preserve the two rivers in question if a WCO did not go ahead, Mr Graham said the process would provide science on the environment, and guidance on how it could be protected.
The process would end with a plan change, which the region would be bound by.
Mr van Beek said he had "good faith that through community processes we're able to look after our rivers and streams and estuaries far better than a locking up mechanism like a WCO which is completely outdated".
Mr van Beek said comments that TANK would not preserve Hawke's Bay rivers was "a slap in the face of the TANK process".
"We're proud of the river that we've got and we've studied it now for three and a half years. It's such a fantastic process, that's why it's such a pity that the WCO wants to cut right across this."
Earlier this week the special tribunal announced it would be splitting the hearing into two parts, with each to consider matters relating to the upper, and lower reaches.
A large number of submitters - including many from the horticulture sector - opposed the WCO on the lower part of the Ngaruroro but supported or were neutral on it for the upper reaches.
Although most of Hawke's Bay's primary production is located in the lower Ngaruroro catchment, these opponents thought they would still oppose a WCO on any part of the river.
At this stage, Mr Graham said he would be opposed to talking about supporting a WCO on the upper river, because he had not spoken with those who would be affected.
"Nobody's even talked to them, nobody has talked to the landowners who are mostly Maori landowners in the upper catchment. It's been a horrendously poor process that has gone on here.
"I'm not going to throw the landowners and the stakeholders in the upper reach of the Ngaruroro under the bus without talking to them and seeing how they feel about this, what does their community feel about this."
Mr Foley said he would not support this because of how the applicants had handled the process, "just because of the bridges they've burned, and the amount of trust they've lost".