HINDMARSH Shire Council has agreed to take ownership of the Dimboola and Jeparit weirs from GWMWater.
Council agreed at a meeting on Wednesday to transfer ownership from GWMWater to the shire after six months of discussion.
Chief executive Dean Miller said ownership was a big decision for council, because the weirs could incur a cost of more than $10 million if they needed to be replaced.
He said despite this, there were many benefits.
"It will eliminate any confusion about the responsibility of operation, maintenance and long-term replacement of the weirs," he said.
"It is also important to the shire that we have functional weirs, where people can participate in water sports and fishing.
"It makes sense that the group that has the most interest in these assets, owns them."
Mr Miller said owning the weirs would also give the community an opportunity to have input on how the weirs were operated.
He said the weirs were significantly damaged during the 2011 floods and were still in need of repair.
"After almost two years of lobbying by council, the Federal Government decided not to fund the repair of these assets because they were not owned by council," he said.
"It was then left up to the State Government to pay for repairs under the National Disaster Fund."
Mr Miller said an allocation of $3.46 million for repairs was made in January.
"Since the floods, it has become evident that GWMWater does not want to be responsible for the weirs," he said.
Mr Miller said council would need to appoint a water manager if there was an outbreak of blue-green algae.
"They would be responsible for testing, water samples and signs, which we don't have the expertise for," he said.
Cr Tony Schneider said ownership was the only real solution to avoid issues with funding.
"We are making a decision for the councils of the future," he said.
"We will have better control of the area and it will complement the community."
Each party will bear their own legal cost and the ownership will not be transferred until repairs to the weirs are completed.
GWMWater's Andrew Rose said the authority would relinquish ownership and responsibility of the weirs to Hindmarsh Shire Council.
"For a long time the weirs have not been required as part of our system and we think they are better managed by another party and the best entity to do that is the shire," he said.
Mr Rose said he was not aware of any other weirs in the Wimmera that GWMWater still owned.