The agreement, signed by the federal and Victorian governments on Tuesday, will deliver 214 gigalitres in water savings.
Under the original deal, the commonwealth and the state were to split the water savings, meaning only half the water saved would be returned to the environment.
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But under the new agreement, Victoria will sell 102 gigalitres of water for environmental use to the federal government.
The irrigation system upgrades, to be rolled out over seven years, will benefit properties across the Goulburn Murray Irrigation District.
Environment Victoria campaigner Juliet Le Feuvre said the deal was positive but added water buybacks would be a cheaper option to
boost the health of the river system.
"It's an expensive way of getting water back into rivers at over $5000 per million litres, much more expensive than buying the water at around $2000 per million litres," Ms Le Feuvre said in a statement.
"This comparison highlights the need for the federal government to continue water purchase programs."
National Irrigators' Council chief executive Danny O'Brien said investment in more efficient irrigation systems would boost farmers' productivity and benefit regional communities.
He said investing in irrigation efficiency allowed farmers to produce the same amount or more food with less water and benefited thousands of people whose jobs and businesses rely on irrigated production.
"Buying water is no doubt cheaper in a strict financial sense but that doesn't factor in the longer-term costs for communities of reduced economic activity," Mr O'Brien said.
Federal Water Minister Tony Burke said the water purchased by the commonwealth would be used to improve the health of Murray-Darling Basin rivers, wetlands and floodplains.
"All of the water saved through this package will be achieved through improved water infrastructure efficiency," he said. "It means irrigators can increase productivity through improved technology, and there is more water to return to our precious environment."
The Baillieu government renegotiated the original agreement with the commonwealth after winning office last November.
Victorian Water Minister Peter Walsh said the deal would help keep water delivery prices down, by offsetting the contribution that irrigators were previously expected to contribute.
