Biosecurity officers are working to reduce the spread of alligator weed which has been on a 30-kilometre stretch of Bendigo Creek.
Conditions in the region for the past two years have been wetter than average and has meant treatment of to prevent the weed has been difficult.
The weed is also state-prohibited, which is the highest category of declared noxious weed across the nation
Agriculture Victoria leading biosecurity officer incursion control Kaitlin Wright said high water levels had prevented weed removal in the most recent autumn and summers.
"Consistent treatment has stopped the infested area from expanding, but the high water levels of the past two years have made thorough treatment difficult," she said.
"It's hoped the seasonal conditions will improve and a more effective control program can return this summer.
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Ms Wright said farmers who have land near Bendigo Creek - especially from the Huntly area onwards - should keep an eye out for alligator weed and report it to Agriculture Victoria.
"Inspect vehicle tyres and equipment if you've been working near the creek," she said.
As well as spreading through high water flows, alligator weed can be transported via vehicle tyres or due to slashing work to maintain drains.
"If mown or cut alligator weed will spread faster as it loves sending out roots from the cuttings," Ms Wright said.
"It's also suspected to be harmful in cattle causing skin blisters and cancers from increased sensitivity to the sun."
Ms Wright said alligator weed has green glossy spear-shaped leaves and hollow stems that range from pale pink to yellow to green.
White papery flowers on stems often resemble common clover flowers but will only be seen in summer.
"The invasive weed can form dense mats that cover large areas of water, push out native plants and reduce bird and fish life," Ms Wright said.
"The weed can also choke drains and damage pumps and irrigation equipment and invade cropland."
Alligator weed has mostly been found in south-east Melbourne backyards, although a few regional backyard infestations have also been detected.
Waterway infestations have previously been found in Melbourne and in regional Victoria, at Bendigo and Warragul.