Water remained high in some areas, including north of Lords Rd, Buchanan Rd and up to Loch Garry Rd.
Shepparton incident controller Ray Jasper said most septic tanks in Bunbartha had filled up and overflowed.
“It’s a nuisance, it’ll smell, but with the amount of water around it dilutes it,” he said.
“It’s just a case of being really careful; if you are cleaning up please wear gloves and the proper PPE.”
At Shepparton, it was possible the Goulburn River could reach the moderate flood level of 10.7m on Thursday, after sitting at 10.6m on Wednesday morning.
It came after rainfall totals up to 80mm fell in the Goulburn River in 24 hours from 9am on Tuesday.
“We had rises in Shepparton, Seymour and Nathalia [on Wednesday night],” Mr Jasper said.
“We’re still pretty comfortable that unless we get one of those really big storms that causes issues, that everything is falling.”
Without wanting to worry residents, Mr Jasper encouraged those with dry, unused sandbags to hold on to them and store them in a dry place, “just in case”.
“It’s not hard to work out we’re in a significant La Niña event, the dams are all full, everything’s saturated,” he said.
“We’re in a situation where it won’t take much unfortunately to prime the rivers and streams again up to some fairly significant flooding.”
At Nathalia, the Broken Creek could reach near the moderate flood level of 2.5m towards the end of the week.
The Seven Creeks at Kialla West was expected to remain above the moderate flood level of 5m on Wednesday, with further rises possible.
At Barmah and Lower Moira, floodwaters had peaked and were falling slowly on Wednesday.
“They’ve had about 36 hours of about the same [flood level] height but the good news is it has dropped 20cm,” Mr Jasper said.
“It will be a slow recession well into the weekend or beyond.”
Murchison Bridge remains open for light vehicles only, with authorities “fairly confident” the footings have moved and are waiting for the water to recede so engineers can assess the situation.
“It’s going to be a bit of a restoration job but we’ll know more next week once they get in there and assess the bridge,” Mr Jasper said.
Meanwhile, the restoration of the Mooroopna Zone Substation is entering the final stages, with some homes and businesses being reconnected to the site after it was flooded last week.
Powercor expects to have all homes and businesses reconnected to the substation by the weekend, depending on final safety inspections.
The substation supplies power to Mooroopna, Tatura, Ardmona, parts of Shepparton, Kialla, Haston, Murchison, Dhurringile, Rushworth and surrounding towns.
CLARIFICATION: The original article published in the News on Thursday, October 27, said a flood warning issued on Wednesday said the sewage treatment plant at Bunbartha had failed.
This was taken from an emergency warning issued on VicEmergency that has since been corrected.
The issue of sewage contaminating floodwaters at Bunbartha is due to septic tanks overflowing.
Goulburn Valley Water has a wastewater management facility at Shepparton, not at Bunbartha, and this has not failed.
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