Testing has found the presence of E coli bacteria in Wellington Harbour, right next to the diving platform.
Signs and caution tape around the popular area for divers warns the public not to swim after testing found "dangerous levels" of the bacteria in the water, according to the Wellington City Council's weekly test.
The results came back last week as "very high", Greater Wellington Regional Council spokesman Stephen Heath said.
The diving platform is near a significant stormwater pipe that drains part of the city which meant the area was always on watch, Heath said.
"We can never absolutely guarantee the site is OK – so we constantly warn people to be careful."
The regional council's water test result for the lagoon would be out on Tuesday, he said.
E coli comes from the intestines of humans and animals, and often comes into water supplies from leaking sewage pipes.
Despite the signs, Greater Wellington Regional Council's interactive water quality tool, which is said to be updated daily, showed green check marks along Wellington Harbour, indicating the water is "suitable for swimming".
Regional Public Health medical officer Dr Jill McKenzie said the warning meant the level of bacteria presented a risk of greater than 10 per cent for stomach bugs, and greater than 4 per cent chance of infection (ear, nose or throat), to those who breathed in contaminated water.
McKenzie said the organisation did not usually receive reports of illness that could be due to E coli contamination as they could be "minor", or it could have been caused by exposure to sick animals or people.
Capital & Coast District Health Board spokesman Chas Te Runa said emergency departments in Wellington were not aware of any cases of infection relating to the bacteria.
Symptoms of E coli bacterial infection include cramps, stomach ache, loss of appetite, nausea and vomiting, fever, diarrhoea and fatigue.
It usually starts three to four days after exposure to the bacteria and lasts a week, though complications can sometimes be quite serious, especially in children.