The appeal was dismissed by the Court of Appeal earlier this month.
The farmers say the appeal, and ECan's determination to set riverbed lines based on 1-in-50 year floods, has cost them, and ratepayers who footed the bill for the appeal, thousands of dollars.
The High Court had earlier determined that ECan's argument over river widths, accepted by the District Court in a prosecution case against Dunsandel dairy farmer Mike Dewhirst, was wrong. ECan's position was based on looking at the river's fullest flow and searching for a suitable bank.
The chairman of the Hurunui-based Rural Advocacy Network, Jamie McFadden says the essential issue was not about protecting braided rivers as ECan purported. It was about using a flawed and unfair process based on hypothetical 1-in-50 year floods to map riverbeds.
''This decision (the appeal) should be celebrated by all those who value common-sense and fair process,'' he says.
Mr McFadden says he cannot understand why ECan, at significant cost to ratepayers, pursued a court case that would have seen land used for houses, roads, and townships, as well as areas farmed for 100 years, deemed riverbed.
''A number of farmers have been subjected to considerable cost - $5000 to $15,000 - and a Waiau farmer prosecuted and branded a criminal because of ECan's flawed, and now proven illegal, riverbed lines policy,'' he says.
He wonders if ECan will show any empathy for the ''appalling injustice it has inflicted on these landowners''.
Dave Holland, who farms near the Hurunui River, says the riverbed lines appeared to be nothing short of a land grab by ECan.
''It is pretty odd when riverbed lines encompass towns and buildings. I can't see how you can suddenly call private property riverbed, and then restrict farming with no talk of compensation or even consultation,'' he says.
He struck problems when he applied for consent to extend his irrigation to a small area of land near the river. ECan said it was riverbed,
''The whole thing has been a waste of money and time. They are trying to land-grab and control what is happening. To all of a sudden call it riverbed was plainly not right,'' he says.
Mr Holland says ECan's riverbed determination defied logic, had cost people quite a lot of money, and it appeared the regional council was running its own agenda without the thought of bringing farmers along with it.
Paul Hood, who farms at Parnassus, paid $10,000 to a surveyor to prove part of the freehold land he had bought alongside the Waiau River, was his land. ECan raised concerns at the 11th hour, after he sought consent to do river protection work on his property, bounding the Waiau River.
''I was told I couldn't farm the land because it was riverbed. It was not until I threatened to take ECan to court, and pointed out their ruling would affect every farmer along the river from Parnassus to Hanmer Springs, that they came around and in the end backed down.''
It was decided to call his property an island, and the consent was issued.
He says he should have challenged it being called an island, but he had just bought the farm and had a cow shed on it.
He said he had spent a considerable amount of money and did not want to put anything at risk for his shareholders.
''I accepted it and moved on.''
• Nadeine Dommisse, ECan's chief operating officer, says there are no plans to appeal the Dewhirst decision.
She says the key reason ECan appealed the decision was to clarify the definition of riverbed under the Resource Management Act (RMA).
''This decision now provides clarity for landowners, communities and river users on a point of law that has wide-reaching implications and is central to ECan's work in protecting the region's much-valued braided rivers.
''The RMA definition of 'bed' is 'the space of land which the waters of the river cover at its fullest flow without overtopping its banks'.
''In our braided rivers, which do not have clearly defined banks, the definition is difficult to apply.''
Ms Dommisse encourages anyone considering works that may be in the bed of a waterway to discuss it with officers before doing any work to ensure a ''fuller understanding of the potential issues''.
''Doing so should help avoid any disputes over whether they are working in a riverbed or not,'' she says.