Now the popular Port Fairy surf spot has been closed and water testing is underway by the Department of Environment, Land, Water and Planning after a brown sludge was detected.

Surfers Tim Dryden and Mark Archbold were in the water every day in the lead-up to the long weekend.

On Good Friday the pair were in the water about an hour apart from one another and saw the brown sludge-like substance in the water.

Two days later, unbeknown to them at the time, they ended up in hospital rooms next to each other both suffering from what doctors believed was a huge hit of bacteria.

Mr Dryden underwent emergency surgery for a perforated bowel, and Mr Archbold was hospitalised for five days.

The Passage is near to Wannon Water's ocean sewage outfall.

An investigation is now underway and the public is advised to avoid the area.

It is not yet clear if the two surfers became sick due to the brown sludge in the water.

READ MORE: Public advised to avoid Port Fairy's The Passage after reports of brown-like substance

Initial evidence of suspected algal blooms has been observed in the surf at two Port Fairy beaches.

The observations were made on Friday afternoon during water collection and monitoring arranged by DELWP's incident management team.

The team was established to respond to reports of a brown sludge-like substance in waters off Port Fairy.

The evidence of suspected algal blooms has been sighted at South Beach and Golfies Beach.

Incident Controller Daniel Sullivan said water samples have been collected from multiple locations and are being tested for algae.

Members of the public are advised to avoid direct contact with waters off the coast of Port Fairy if they observe discolouration in the water," he said.

"Anyone who experiences illness after coming into contact with discoloured water in this area should seek medical advice.

"An update will be provided to the community once the test results are available."

Mr Archbold was paddling out into the swell on Good Friday when he noticed some "semi-solid milky brown stuff that was mucusy to touch".

A surfer nearby joked it was sewage.

"Friday afternoon I had been out a while when I noticed all this stuff through the water, not just on top but throughout the water," he said.

"I was pretty disgusted, I caught the next wave in.

"Around 2.30am Saturday morning I got up with an insane headache, I couldn't even walk or support myself. I had fevers and felt like absolute crap.

"So I got some electrolytes in me and tried to sleep it off. By the morning I went straight down to emergency. I was that crook they started bags of antibiotics and fluid straight away.

"I was in there for five days. They said my white blood cells were through the roof and the doctor said my body had copped a massive hit of bacteria from somewhere.

"I had pneumonia in my lung, an infected sinus and prostate and fluid around my kidneys.

"It just smashed me where it could."

Mr Archbold said he lodged a complaint to the Environment Protection Authority and was told the case was closed before anyone had visited the site.

"It was unbelievable," he said.

EPA South West regional manager Carolyn Francis said it received the report on April 9.

She said there were both natural and incident-related reasons why water could be discoloured, and EPA encouraged the public to report suspected pollution as soon as possible.

"The Wannon Water Port Fairy Wastewater Treatment Plant operates under an EPA licence that requires it to notify EPA of any issues. No notifications have been received for this period of time.

"The EPA licence also requires a comprehensive testing program to be conducted by Wannon Water.

"If there are any compliance issues with the plant, Wannon Water is required to notify EPA immediately. Depending on the nature of the incident and potential for environmental or public health impact, EPA would determine whether any Wannon Water communication is required to notify the public of the issue."

Before the Easter weekend fellow surfer Tim Dryden was an active, healthy 51-year-old.

After his emergency surgery he faces at least six months with a colostomy bag and the rest of the year out of work.

He wants to see a full investigation into the potential connection between the poor water quality and his sharp health decline.

"Basically what happened with me on Friday is I went for a surf at The Passage, and got out about an hour from when Mark got in," he said.

"I didn't have any trouble until Sunday when I woke up feeling crappy in the guts which then escalated.

"I went to the emergency department but they were so busy so I went home. I then woke up two hours later much worse and went straight through to emergency surgery.

"I had a perforated bowel and spent three hours on the table. I woke up with a colostomy bag and a heap of holes in me.

"I've never had trouble in that area before.

"I had a massive infection that had travelled through me and found my weakest point.

"I'm three months from lifting anything, and in six months they have to reattach everything."

Mr Dryden is a supervisor at Warrnambool Cheese and Butter and is facing the prospect of being out of work for the rest of the year.

"They're saying I could have died if I hadn't gone back to emergency, it could have gone real bad," Mr Dryden said.

"It's going to be a pretty hard road to get back from that.

"I can't lift anything for months, it's going to be a big financial hit to me."

He and Mr Archbold only made the connection when their partners, who both work on the Moyneyana Festival, were talking and realised their husbands both ended up in hospital after surfing at The Passage.

"What are the chances of him and me surfing an hour apart, on the same day, and we both ended up on the same ward?

"I'm still coming to terms with what's happened to me, I want to stop it from happening to anyone else."

Treated water produced at the Port Fairy Sewage Treatment Plant is discharged in an ocean mixing zone under a licence issued by the EPA.

Wannon Water told The Standard it conducted extensive tests of the ocean water around the outfall to ensure it continued to comply with the licence conditions.

"Wannon Water has not experienced any issues with our Port Fairy Sewage Treatment Plant or the outfall," a spokeswoman said.

South-west volunteers conducted a clean-up from Warrnambool through to The Cutting this week and found sanitary items washed up on the beach.

They only started to notice sanitary items when they reached The Cutting at Port Fairy.

Warrnambool resident Colleen Hughson cleans the site with other Beach Patrol 3280 volunteers once a week and said it was unusual to see items like that.

"The items included sanitary pads, tampons, wipes and cotton buds and could be seen along the fresh tide line and caught up in the weed that had washed in," she said.

"We believe the items have come from a local source because the items were 'fresh' and in a concentrated area."

It's not clear whether the items are connected to the nearby sewage ocean outfall, but Ms Hughson said authorities had a duty to notify the public of any contamination.

"When it comes to the health and wellbeing of our local community I believe Wannon Water need to go beyond what is required of them in their EPA licence and protect our community," she said.

"After the series of documented dirty decants from the Warrnambool outfall Wannon Water was given a directive from the EPA to notify the public if and when a dirty decant occurred."

An EPA spokesman said that given the time between the discoloured water being seen, and it being reported to EPA, any EPA field response to identify a source or undertake sampling was not possible.

"An EPA officer was actually in the area yesterday and did not observe any discoloured water," he said on Friday.

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