However, an anti-dredging group attributed murky water detected off Hobsons Bay to sludge being excreted from the Yarra River.

Monitor Mick Bourke said that on June 10, turbidity levels at a monitoring buoy in Hobsons Bay exceeded the channel-deepening project's "response level one".

Under an environmental management plan, response levels one and two are in place as early-warning systems to alert the dredging company, Port of Melbourne Corporation and the Office of the Environmental Monitor.

Excess turbidity can adversely affect plants and animals such as seagrass, seabirds and fish.

Mr Bourke said this month's elevated reading was caused by weather, including strong winds and rain across Melbourne's catchment.

"The dredge vessels were not operating in Hobsons Bay at the time and the office noted that turbidity returned to background levels at this site once the weather conditions eased," he said.

Blue Wedges president Jenny Warfe said Mr Bourke's explanation "conveniently ignored" the continual dredging under way in the Yarra River.

"Where else can murky and toxic Yarra sludge go other than into Hobsons Bay?" she asked.

"We have had several recent reports of highly turbid water in the Yarra emanating from the dredges - it has to end up in Hobsons Bay, doesn't it?

"Perhaps Mr Bourke expects us to believe that the murky water in Hobsons Bay couldn't possibly be related to murky sludge being dredged up in the Yarra. If so, he must think we are fools."

Turbidity levels also exceeded environmental limits on November 22 at the mouth of the Yarra River and on April 26 in the south of the bay.